Chapter 16 Testing completeness correction before calculating distilling GIFTs
16.1 Load MG data
load("data/data_mg.Rdata")
# Load raw genome annotations
genome_annotations <- read_tsv("data/gene_annotations.tsv.xz")
gifts_raw <- distill(genome_annotations, GIFT_db2,
genomecol = 2, annotcol = c(9,10,19), verbosity = F)
Identifiers in the annotation table: 1570
Identifiers in the database: 1547
Identifiers in both: 239
Percentage of annotation table identifiers used for distillation: 15.22%
Percentage of database identifiers used for distillation: 15.45%# Load ENA to genome_id table
ena_to_mag_id <- read_tsv("data/ena_to_mag_id.tsv")
gifts_matrix <-
gifts_raw %>%
data.frame() %>%
rownames_to_column(var = 'mag_name') %>%
left_join(ena_to_mag_id %>%
select(mag_name, mag_id),
by = 'mag_name') %>%
select(-mag_name) %>%
relocate(mag_id) %>%
filter(mag_id %in% genome_taxonomy$genome) %>%
column_to_rownames('mag_id') %>%
as.matrix()
genome_completeness <-
genome_stats %>%
select(genome, completeness_score) %>%
as.matrix()16.2 Define function for correction
# Correction function defined in
# https://github.com/anttonalberdi/DAMMA/blob/main/R/damma_correction.R
# Based on https://www.nature.com/articles/s43705-023-00221-z
gifts_correction <- function(MCI_table, genome_completeness, stats = TRUE) {
#Sort Genomes and test matching
MCI_table <- MCI_table[order(rownames(MCI_table)),]
genome_completeness <- genome_completeness[order(genome_completeness[,1]),]
if (all(as.character(rownames(MCI_table)) !=
as.character(genome_completeness[,1])))
stop("Pathway table is missing")
#Get completeness values
Genome_completeness <- as.numeric(genome_completeness[,2])
#Create corrected fullness matrix
MCI_table_corrected <- matrix(0,nrow = nrow(MCI_table),ncol = ncol(MCI_table))
colnames(MCI_table_corrected) = colnames(MCI_table)
rownames(MCI_table_corrected) = rownames(MCI_table)
#Iterate modelling and correction for each function
suppressWarnings(
for (i in 1:ncol(MCI_table)) {
Model <- glm(MCI_table[,i]~Genome_completeness,family = "binomial")
slope_coef <- coef(Model)[2]
if (slope_coef > 0) {
for (j in 1:nrow(MCI_table)) {
# Model prediction of fullness if completeness was 100%
pred_100 <- round(predict(Model,
newdata = data.frame(
Genome_completeness = 100),
type = "response"),1)
# Model prediction of fullness for actual completeness of the focal MAG
pred_focal <- round(predict(Model,
newdata = data.frame(
Genome_completeness = Genome_completeness[j]),
type = "response"), 1)
# The expected change in function fullness if focal MAG was 100% complete
pred_diff <- pred_100 - pred_focal
MCI_table_corrected[j,i] = MCI_table[j,i] + pred_diff
}
} else if (slope_coef <= 0) {
MCI_table_corrected[,i] <- MCI_table[,i]
}
}
)
# If corrected fullness >1, convert it to 1.
MCI_table_corrected[MCI_table_corrected > 1] <- 1
# Outout overall correction statistics on screen
total <- nrow(MCI_table)*ncol(MCI_table)
changes <- c(MCI_table == MCI_table_corrected)
changes <- length(changes[!(changes)])
percentage <- round(changes / total * 100,1)
cat(paste0(changes," out of ",total," (",percentage,"%) fullness values were corrected\n"))
if (stats == TRUE) {
#Outout overall correction statistics on screen
total <- ncol(MCI_table_corrected)
for (r in rownames(MCI_table_corrected)) {
completeness <- round(as.numeric(genome_completeness[genome_completeness[,1] == r,2]),1)
changes <- MCI_table[r,] == MCI_table_corrected[r,]
changes <- length(changes[!(changes)])
percentage <- round(changes / total * 100,1)
cat(paste0("\t",r," (",completeness,"%): ",changes,
"/",total," (",percentage,"%) fullness values were corrected\n"))
}
}
#Output corrected table
return(MCI_table_corrected)
}16.3 Calculate corrected GIFTs
77385 out of 258930 (29.9%) fullness values were corrected
cmag_001 (90.5%): 104/315 (33%) fullness values were corrected
cmag_002 (98%): 38/315 (12.1%) fullness values were corrected
cmag_003 (64%): 180/315 (57.1%) fullness values were corrected
cmag_004 (92.7%): 113/315 (35.9%) fullness values were corrected
cmag_005 (52.1%): 183/315 (58.1%) fullness values were corrected
cmag_006 (99.3%): 12/315 (3.8%) fullness values were corrected
cmag_007 (97.3%): 50/315 (15.9%) fullness values were corrected
cmag_008 (90.4%): 117/315 (37.1%) fullness values were corrected
cmag_009 (98.7%): 28/315 (8.9%) fullness values were corrected
cmag_010 (97.3%): 47/315 (14.9%) fullness values were corrected
cmag_011 (93.3%): 108/315 (34.3%) fullness values were corrected
cmag_012 (94.8%): 80/315 (25.4%) fullness values were corrected
cmag_013 (86.1%): 146/315 (46.3%) fullness values were corrected
cmag_014 (82.5%): 153/315 (48.6%) fullness values were corrected
cmag_015 (80.3%): 158/315 (50.2%) fullness values were corrected
cmag_016 (79.4%): 155/315 (49.2%) fullness values were corrected
cmag_017 (99.3%): 11/315 (3.5%) fullness values were corrected
cmag_018 (75.4%): 164/315 (52.1%) fullness values were corrected
cmag_019 (94%): 95/315 (30.2%) fullness values were corrected
cmag_020 (93.4%): 83/315 (26.3%) fullness values were corrected
cmag_021 (99.2%): 16/315 (5.1%) fullness values were corrected
cmag_022 (72.2%): 173/315 (54.9%) fullness values were corrected
cmag_023 (98.7%): 23/315 (7.3%) fullness values were corrected
cmag_024 (96%): 63/315 (20%) fullness values were corrected
cmag_025 (99.1%): 9/315 (2.9%) fullness values were corrected
cmag_026 (80.1%): 144/315 (45.7%) fullness values were corrected
cmag_027 (93.6%): 98/315 (31.1%) fullness values were corrected
cmag_028 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_029 (92.7%): 114/315 (36.2%) fullness values were corrected
cmag_030 (95.4%): 80/315 (25.4%) fullness values were corrected
cmag_031 (70.3%): 164/315 (52.1%) fullness values were corrected
cmag_032 (73.3%): 163/315 (51.7%) fullness values were corrected
cmag_033 (76.9%): 164/315 (52.1%) fullness values were corrected
cmag_034 (92%): 97/315 (30.8%) fullness values were corrected
cmag_035 (97.7%): 42/315 (13.3%) fullness values were corrected
cmag_036 (97.4%): 44/315 (14%) fullness values were corrected
cmag_037 (95.6%): 76/315 (24.1%) fullness values were corrected
cmag_038 (94%): 77/315 (24.4%) fullness values were corrected
cmag_039 (98.7%): 22/315 (7%) fullness values were corrected
cmag_040 (64.1%): 171/315 (54.3%) fullness values were corrected
cmag_041 (94%): 91/315 (28.9%) fullness values were corrected
cmag_042 (74.9%): 147/315 (46.7%) fullness values were corrected
cmag_043 (85.3%): 129/315 (41%) fullness values were corrected
cmag_044 (72.1%): 162/315 (51.4%) fullness values were corrected
cmag_045 (100%): 0/315 (0%) fullness values were corrected
cmag_046 (89.7%): 115/315 (36.5%) fullness values were corrected
cmag_047 (92.7%): 105/315 (33.3%) fullness values were corrected
cmag_048 (98.7%): 26/315 (8.3%) fullness values were corrected
cmag_049 (94.8%): 80/315 (25.4%) fullness values were corrected
cmag_050 (95.4%): 65/315 (20.6%) fullness values were corrected
cmag_051 (71.1%): 165/315 (52.4%) fullness values were corrected
cmag_052 (80.3%): 157/315 (49.8%) fullness values were corrected
cmag_053 (92.6%): 99/315 (31.4%) fullness values were corrected
cmag_054 (75%): 165/315 (52.4%) fullness values were corrected
cmag_055 (92.6%): 113/315 (35.9%) fullness values were corrected
cmag_056 (88.8%): 136/315 (43.2%) fullness values were corrected
cmag_057 (98.7%): 29/315 (9.2%) fullness values were corrected
cmag_058 (90.5%): 115/315 (36.5%) fullness values were corrected
cmag_059 (99%): 18/315 (5.7%) fullness values were corrected
cmag_060 (96.4%): 57/315 (18.1%) fullness values were corrected
cmag_061 (63.8%): 178/315 (56.5%) fullness values were corrected
cmag_062 (93.2%): 87/315 (27.6%) fullness values were corrected
cmag_063 (63.1%): 163/315 (51.7%) fullness values were corrected
cmag_064 (99%): 17/315 (5.4%) fullness values were corrected
cmag_065 (98.2%): 29/315 (9.2%) fullness values were corrected
cmag_066 (85.4%): 122/315 (38.7%) fullness values were corrected
cmag_067 (98.6%): 26/315 (8.3%) fullness values were corrected
cmag_068 (76.3%): 168/315 (53.3%) fullness values were corrected
cmag_069 (93.3%): 107/315 (34%) fullness values were corrected
cmag_070 (53.9%): 182/315 (57.8%) fullness values were corrected
cmag_071 (99%): 18/315 (5.7%) fullness values were corrected
cmag_072 (66.7%): 176/315 (55.9%) fullness values were corrected
cmag_073 (91.9%): 104/315 (33%) fullness values were corrected
cmag_074 (94.2%): 83/315 (26.3%) fullness values were corrected
cmag_075 (93.6%): 85/315 (27%) fullness values were corrected
cmag_076 (96.4%): 56/315 (17.8%) fullness values were corrected
cmag_077 (97.8%): 43/315 (13.7%) fullness values were corrected
cmag_078 (89.6%): 116/315 (36.8%) fullness values were corrected
cmag_079 (96.7%): 58/315 (18.4%) fullness values were corrected
cmag_080 (100%): 0/315 (0%) fullness values were corrected
cmag_081 (99.3%): 11/315 (3.5%) fullness values were corrected
cmag_082 (99.3%): 12/315 (3.8%) fullness values were corrected
cmag_083 (90.9%): 102/315 (32.4%) fullness values were corrected
cmag_084 (97.3%): 46/315 (14.6%) fullness values were corrected
cmag_085 (90.3%): 128/315 (40.6%) fullness values were corrected
cmag_086 (93.8%): 93/315 (29.5%) fullness values were corrected
cmag_087 (88.5%): 111/315 (35.2%) fullness values were corrected
cmag_088 (85.6%): 142/315 (45.1%) fullness values were corrected
cmag_089 (98.6%): 24/315 (7.6%) fullness values were corrected
cmag_090 (89.3%): 135/315 (42.9%) fullness values were corrected
cmag_091 (96%): 62/315 (19.7%) fullness values were corrected
cmag_092 (91.3%): 111/315 (35.2%) fullness values were corrected
cmag_093 (74%): 163/315 (51.7%) fullness values were corrected
cmag_094 (95.4%): 64/315 (20.3%) fullness values were corrected
cmag_095 (98.6%): 27/315 (8.6%) fullness values were corrected
cmag_096 (94.3%): 84/315 (26.7%) fullness values were corrected
cmag_097 (95.6%): 67/315 (21.3%) fullness values were corrected
cmag_098 (95.6%): 68/315 (21.6%) fullness values were corrected
cmag_099 (72.5%): 157/315 (49.8%) fullness values were corrected
cmag_100 (98.1%): 36/315 (11.4%) fullness values were corrected
cmag_101 (95.8%): 61/315 (19.4%) fullness values were corrected
cmag_102 (99.4%): 12/315 (3.8%) fullness values were corrected
cmag_103 (51.9%): 184/315 (58.4%) fullness values were corrected
cmag_104 (100%): 0/315 (0%) fullness values were corrected
cmag_105 (91.8%): 100/315 (31.7%) fullness values were corrected
cmag_106 (89.7%): 133/315 (42.2%) fullness values were corrected
cmag_107 (85.4%): 149/315 (47.3%) fullness values were corrected
cmag_108 (90.1%): 115/315 (36.5%) fullness values were corrected
cmag_109 (93.8%): 101/315 (32.1%) fullness values were corrected
cmag_110 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_111 (90.9%): 112/315 (35.6%) fullness values were corrected
cmag_112 (99.4%): 11/315 (3.5%) fullness values were corrected
cmag_113 (79%): 146/315 (46.3%) fullness values were corrected
cmag_114 (97.9%): 45/315 (14.3%) fullness values were corrected
cmag_115 (99.7%): 8/315 (2.5%) fullness values were corrected
cmag_116 (54.5%): 181/315 (57.5%) fullness values were corrected
cmag_117 (99.4%): 8/315 (2.5%) fullness values were corrected
cmag_118 (66.4%): 173/315 (54.9%) fullness values were corrected
cmag_119 (76.1%): 164/315 (52.1%) fullness values were corrected
cmag_120 (95.3%): 68/315 (21.6%) fullness values were corrected
cmag_121 (92.6%): 108/315 (34.3%) fullness values were corrected
cmag_122 (85.7%): 130/315 (41.3%) fullness values were corrected
cmag_123 (96.3%): 58/315 (18.4%) fullness values were corrected
cmag_124 (84%): 149/315 (47.3%) fullness values were corrected
cmag_125 (97.2%): 54/315 (17.1%) fullness values were corrected
cmag_126 (98.1%): 34/315 (10.8%) fullness values were corrected
cmag_127 (64.2%): 167/315 (53%) fullness values were corrected
cmag_128 (99.3%): 12/315 (3.8%) fullness values were corrected
cmag_129 (74.2%): 155/315 (49.2%) fullness values were corrected
cmag_130 (98.7%): 24/315 (7.6%) fullness values were corrected
cmag_131 (78.8%): 161/315 (51.1%) fullness values were corrected
cmag_132 (72.4%): 173/315 (54.9%) fullness values were corrected
cmag_133 (99.2%): 13/315 (4.1%) fullness values were corrected
cmag_134 (69.8%): 164/315 (52.1%) fullness values were corrected
cmag_135 (92.3%): 96/315 (30.5%) fullness values were corrected
cmag_136 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_137 (83%): 136/315 (43.2%) fullness values were corrected
cmag_138 (84.3%): 124/315 (39.4%) fullness values were corrected
cmag_139 (85.5%): 130/315 (41.3%) fullness values were corrected
cmag_140 (95.2%): 78/315 (24.8%) fullness values were corrected
cmag_141 (80.9%): 156/315 (49.5%) fullness values were corrected
cmag_142 (98%): 40/315 (12.7%) fullness values were corrected
cmag_143 (95.7%): 70/315 (22.2%) fullness values were corrected
cmag_144 (82%): 152/315 (48.3%) fullness values were corrected
cmag_145 (91.6%): 105/315 (33.3%) fullness values were corrected
cmag_146 (97.4%): 52/315 (16.5%) fullness values were corrected
cmag_147 (84.1%): 128/315 (40.6%) fullness values were corrected
cmag_148 (86.5%): 132/315 (41.9%) fullness values were corrected
cmag_149 (92.7%): 114/315 (36.2%) fullness values were corrected
cmag_150 (92.1%): 118/315 (37.5%) fullness values were corrected
cmag_151 (75.9%): 162/315 (51.4%) fullness values were corrected
cmag_152 (67.6%): 170/315 (54%) fullness values were corrected
cmag_153 (99.4%): 11/315 (3.5%) fullness values were corrected
cmag_154 (56.7%): 181/315 (57.5%) fullness values were corrected
cmag_155 (100%): 0/315 (0%) fullness values were corrected
cmag_156 (63.5%): 175/315 (55.6%) fullness values were corrected
cmag_157 (80%): 159/315 (50.5%) fullness values were corrected
cmag_158 (75%): 163/315 (51.7%) fullness values were corrected
cmag_159 (62.5%): 153/315 (48.6%) fullness values were corrected
cmag_160 (92.5%): 88/315 (27.9%) fullness values were corrected
cmag_161 (92.7%): 104/315 (33%) fullness values were corrected
cmag_162 (98.3%): 30/315 (9.5%) fullness values were corrected
cmag_163 (63.5%): 184/315 (58.4%) fullness values were corrected
cmag_164 (91.6%): 119/315 (37.8%) fullness values were corrected
cmag_165 (76.7%): 165/315 (52.4%) fullness values were corrected
cmag_166 (97.8%): 43/315 (13.7%) fullness values were corrected
cmag_167 (97.2%): 26/315 (8.3%) fullness values were corrected
cmag_168 (98.7%): 21/315 (6.7%) fullness values were corrected
cmag_169 (92.7%): 114/315 (36.2%) fullness values were corrected
cmag_170 (93.2%): 86/315 (27.3%) fullness values were corrected
cmag_171 (75%): 164/315 (52.1%) fullness values were corrected
cmag_172 (97.3%): 48/315 (15.2%) fullness values were corrected
cmag_173 (95.1%): 70/315 (22.2%) fullness values were corrected
cmag_174 (80.2%): 148/315 (47%) fullness values were corrected
cmag_175 (100%): 0/315 (0%) fullness values were corrected
cmag_176 (74.3%): 153/315 (48.6%) fullness values were corrected
cmag_177 (98%): 34/315 (10.8%) fullness values were corrected
cmag_178 (84%): 126/315 (40%) fullness values were corrected
cmag_179 (93.3%): 89/315 (28.3%) fullness values were corrected
cmag_180 (97.9%): 39/315 (12.4%) fullness values were corrected
cmag_181 (99.3%): 14/315 (4.4%) fullness values were corrected
cmag_182 (98%): 37/315 (11.7%) fullness values were corrected
cmag_183 (77.9%): 155/315 (49.2%) fullness values were corrected
cmag_184 (89.4%): 115/315 (36.5%) fullness values were corrected
cmag_185 (95.4%): 67/315 (21.3%) fullness values were corrected
cmag_186 (98.1%): 33/315 (10.5%) fullness values were corrected
cmag_187 (99.5%): 8/315 (2.5%) fullness values were corrected
cmag_188 (91.5%): 120/315 (38.1%) fullness values were corrected
cmag_189 (89.3%): 136/315 (43.2%) fullness values were corrected
cmag_190 (90.3%): 110/315 (34.9%) fullness values were corrected
cmag_191 (67.5%): 178/315 (56.5%) fullness values were corrected
cmag_192 (83.9%): 149/315 (47.3%) fullness values were corrected
cmag_193 (96.2%): 58/315 (18.4%) fullness values were corrected
cmag_194 (90.2%): 123/315 (39%) fullness values were corrected
cmag_195 (64.1%): 177/315 (56.2%) fullness values were corrected
cmag_196 (67.2%): 167/315 (53%) fullness values were corrected
cmag_197 (95.7%): 58/315 (18.4%) fullness values were corrected
cmag_198 (98.3%): 32/315 (10.2%) fullness values were corrected
cmag_199 (81.5%): 155/315 (49.2%) fullness values were corrected
cmag_200 (96.8%): 61/315 (19.4%) fullness values were corrected
cmag_201 (50.9%): 171/315 (54.3%) fullness values were corrected
cmag_202 (97.7%): 39/315 (12.4%) fullness values were corrected
cmag_203 (80.6%): 148/315 (47%) fullness values were corrected
cmag_204 (60.6%): 176/315 (55.9%) fullness values were corrected
cmag_205 (59.4%): 177/315 (56.2%) fullness values were corrected
cmag_206 (97.8%): 48/315 (15.2%) fullness values were corrected
cmag_207 (96.7%): 54/315 (17.1%) fullness values were corrected
cmag_208 (90.6%): 117/315 (37.1%) fullness values were corrected
cmag_209 (97.3%): 47/315 (14.9%) fullness values were corrected
cmag_210 (70.8%): 171/315 (54.3%) fullness values were corrected
cmag_211 (97.4%): 41/315 (13%) fullness values were corrected
cmag_212 (69.5%): 165/315 (52.4%) fullness values were corrected
cmag_213 (71.7%): 175/315 (55.6%) fullness values were corrected
cmag_214 (99.3%): 11/315 (3.5%) fullness values were corrected
cmag_215 (88.8%): 135/315 (42.9%) fullness values were corrected
cmag_216 (98.8%): 18/315 (5.7%) fullness values were corrected
cmag_217 (56.1%): 182/315 (57.8%) fullness values were corrected
cmag_218 (94.8%): 76/315 (24.1%) fullness values were corrected
cmag_219 (98.7%): 21/315 (6.7%) fullness values were corrected
cmag_220 (99.4%): 9/315 (2.9%) fullness values were corrected
cmag_221 (97.3%): 43/315 (13.7%) fullness values were corrected
cmag_222 (73.4%): 160/315 (50.8%) fullness values were corrected
cmag_223 (99.6%): 7/315 (2.2%) fullness values were corrected
cmag_224 (95.3%): 73/315 (23.2%) fullness values were corrected
cmag_225 (85.6%): 127/315 (40.3%) fullness values were corrected
cmag_226 (59.2%): 175/315 (55.6%) fullness values were corrected
cmag_227 (95.5%): 69/315 (21.9%) fullness values were corrected
cmag_228 (99.2%): 15/315 (4.8%) fullness values were corrected
cmag_229 (100%): 0/315 (0%) fullness values were corrected
cmag_230 (85.3%): 147/315 (46.7%) fullness values were corrected
cmag_231 (89.1%): 122/315 (38.7%) fullness values were corrected
cmag_232 (88.9%): 121/315 (38.4%) fullness values were corrected
cmag_233 (53.3%): 175/315 (55.6%) fullness values were corrected
cmag_234 (61%): 179/315 (56.8%) fullness values were corrected
cmag_235 (97.3%): 45/315 (14.3%) fullness values were corrected
cmag_236 (94%): 80/315 (25.4%) fullness values were corrected
cmag_237 (95.3%): 74/315 (23.5%) fullness values were corrected
cmag_238 (97%): 48/315 (15.2%) fullness values were corrected
cmag_239 (57.4%): 174/315 (55.2%) fullness values were corrected
cmag_240 (97.3%): 49/315 (15.6%) fullness values were corrected
cmag_241 (98.7%): 24/315 (7.6%) fullness values were corrected
cmag_242 (74.6%): 163/315 (51.7%) fullness values were corrected
cmag_243 (99%): 21/315 (6.7%) fullness values were corrected
cmag_244 (95.3%): 72/315 (22.9%) fullness values were corrected
cmag_245 (99.4%): 8/315 (2.5%) fullness values were corrected
cmag_246 (74.4%): 164/315 (52.1%) fullness values were corrected
cmag_247 (92.4%): 93/315 (29.5%) fullness values were corrected
cmag_248 (99.6%): 7/315 (2.2%) fullness values were corrected
cmag_249 (88.8%): 136/315 (43.2%) fullness values were corrected
cmag_250 (98.4%): 33/315 (10.5%) fullness values were corrected
cmag_251 (85.3%): 130/315 (41.3%) fullness values were corrected
cmag_252 (100%): 0/315 (0%) fullness values were corrected
cmag_253 (89%): 117/315 (37.1%) fullness values were corrected
cmag_254 (90.2%): 106/315 (33.7%) fullness values were corrected
cmag_255 (93.9%): 86/315 (27.3%) fullness values were corrected
cmag_256 (95.2%): 77/315 (24.4%) fullness values were corrected
cmag_257 (97.8%): 40/315 (12.7%) fullness values were corrected
cmag_258 (90.6%): 99/315 (31.4%) fullness values were corrected
cmag_259 (99.1%): 15/315 (4.8%) fullness values were corrected
cmag_260 (89.8%): 114/315 (36.2%) fullness values were corrected
cmag_261 (71.9%): 169/315 (53.7%) fullness values were corrected
cmag_262 (93.1%): 91/315 (28.9%) fullness values were corrected
cmag_263 (90.8%): 123/315 (39%) fullness values were corrected
cmag_264 (73.6%): 173/315 (54.9%) fullness values were corrected
cmag_265 (61.4%): 177/315 (56.2%) fullness values were corrected
cmag_266 (98.7%): 25/315 (7.9%) fullness values were corrected
cmag_267 (98.2%): 39/315 (12.4%) fullness values were corrected
cmag_268 (95.3%): 71/315 (22.5%) fullness values were corrected
cmag_269 (69.2%): 167/315 (53%) fullness values were corrected
cmag_270 (62.9%): 181/315 (57.5%) fullness values were corrected
cmag_271 (98.5%): 23/315 (7.3%) fullness values were corrected
cmag_272 (75.4%): 167/315 (53%) fullness values were corrected
cmag_273 (69%): 167/315 (53%) fullness values were corrected
cmag_275 (52.8%): 181/315 (57.5%) fullness values were corrected
cmag_276 (91%): 122/315 (38.7%) fullness values were corrected
cmag_277 (92.7%): 92/315 (29.2%) fullness values were corrected
cmag_278 (59.4%): 169/315 (53.7%) fullness values were corrected
cmag_279 (91.1%): 109/315 (34.6%) fullness values were corrected
cmag_280 (59.6%): 184/315 (58.4%) fullness values were corrected
cmag_281 (95.6%): 73/315 (23.2%) fullness values were corrected
cmag_282 (82.1%): 142/315 (45.1%) fullness values were corrected
cmag_283 (69.3%): 167/315 (53%) fullness values were corrected
cmag_284 (92.1%): 119/315 (37.8%) fullness values were corrected
cmag_285 (94.3%): 83/315 (26.3%) fullness values were corrected
cmag_286 (93.3%): 96/315 (30.5%) fullness values were corrected
cmag_287 (72.3%): 174/315 (55.2%) fullness values were corrected
cmag_288 (95.3%): 71/315 (22.5%) fullness values were corrected
cmag_289 (99.8%): 8/315 (2.5%) fullness values were corrected
cmag_290 (92.7%): 112/315 (35.6%) fullness values were corrected
cmag_291 (97.3%): 45/315 (14.3%) fullness values were corrected
cmag_292 (86.4%): 139/315 (44.1%) fullness values were corrected
cmag_293 (93.6%): 92/315 (29.2%) fullness values were corrected
cmag_294 (80.8%): 157/315 (49.8%) fullness values were corrected
cmag_295 (98.6%): 27/315 (8.6%) fullness values were corrected
cmag_296 (79.7%): 154/315 (48.9%) fullness values were corrected
cmag_297 (94.8%): 75/315 (23.8%) fullness values were corrected
cmag_298 (99.4%): 10/315 (3.2%) fullness values were corrected
cmag_299 (100%): 0/315 (0%) fullness values were corrected
cmag_300 (98.1%): 37/315 (11.7%) fullness values were corrected
cmag_301 (83%): 153/315 (48.6%) fullness values were corrected
cmag_302 (74.7%): 169/315 (53.7%) fullness values were corrected
cmag_303 (91.5%): 121/315 (38.4%) fullness values were corrected
cmag_304 (64.9%): 160/315 (50.8%) fullness values were corrected
cmag_305 (85.4%): 147/315 (46.7%) fullness values were corrected
cmag_306 (70.7%): 159/315 (50.5%) fullness values were corrected
cmag_307 (94.9%): 90/315 (28.6%) fullness values were corrected
cmag_308 (97.3%): 49/315 (15.6%) fullness values were corrected
cmag_309 (92.2%): 94/315 (29.8%) fullness values were corrected
cmag_310 (98.7%): 23/315 (7.3%) fullness values were corrected
cmag_311 (94.9%): 90/315 (28.6%) fullness values were corrected
cmag_312 (89.7%): 114/315 (36.2%) fullness values were corrected
cmag_313 (82.4%): 149/315 (47.3%) fullness values were corrected
cmag_314 (97.9%): 29/315 (9.2%) fullness values were corrected
cmag_315 (96.8%): 47/315 (14.9%) fullness values were corrected
cmag_316 (71.1%): 177/315 (56.2%) fullness values were corrected
cmag_317 (83%): 151/315 (47.9%) fullness values were corrected
cmag_318 (82.7%): 152/315 (48.3%) fullness values were corrected
cmag_319 (62.7%): 184/315 (58.4%) fullness values were corrected
cmag_320 (99.2%): 10/315 (3.2%) fullness values were corrected
cmag_321 (91.4%): 109/315 (34.6%) fullness values were corrected
cmag_322 (94.9%): 74/315 (23.5%) fullness values were corrected
cmag_323 (71.9%): 173/315 (54.9%) fullness values were corrected
cmag_324 (94%): 73/315 (23.2%) fullness values were corrected
cmag_325 (90.9%): 95/315 (30.2%) fullness values were corrected
cmag_326 (96.9%): 50/315 (15.9%) fullness values were corrected
cmag_327 (73.9%): 162/315 (51.4%) fullness values were corrected
cmag_328 (82.7%): 138/315 (43.8%) fullness values were corrected
cmag_329 (98.7%): 23/315 (7.3%) fullness values were corrected
cmag_330 (85.8%): 133/315 (42.2%) fullness values were corrected
cmag_331 (89.7%): 115/315 (36.5%) fullness values were corrected
cmag_332 (99.8%): 7/315 (2.2%) fullness values were corrected
cmag_333 (89.7%): 114/315 (36.2%) fullness values were corrected
cmag_334 (69.5%): 173/315 (54.9%) fullness values were corrected
cmag_335 (94.4%): 78/315 (24.8%) fullness values were corrected
cmag_336 (92.3%): 94/315 (29.8%) fullness values were corrected
cmag_337 (92.9%): 91/315 (28.9%) fullness values were corrected
cmag_338 (99.3%): 12/315 (3.8%) fullness values were corrected
cmag_339 (94.8%): 79/315 (25.1%) fullness values were corrected
cmag_340 (78%): 156/315 (49.5%) fullness values were corrected
cmag_341 (60%): 168/315 (53.3%) fullness values were corrected
cmag_342 (94.8%): 80/315 (25.4%) fullness values were corrected
cmag_343 (79%): 143/315 (45.4%) fullness values were corrected
cmag_344 (94.1%): 79/315 (25.1%) fullness values were corrected
cmag_345 (98.8%): 19/315 (6%) fullness values were corrected
cmag_346 (95.2%): 77/315 (24.4%) fullness values were corrected
cmag_347 (77%): 144/315 (45.7%) fullness values were corrected
cmag_348 (97.3%): 58/315 (18.4%) fullness values were corrected
cmag_349 (96.4%): 59/315 (18.7%) fullness values were corrected
cmag_350 (78.7%): 162/315 (51.4%) fullness values were corrected
cmag_351 (99.8%): 4/315 (1.3%) fullness values were corrected
cmag_352 (97.7%): 41/315 (13%) fullness values were corrected
cmag_353 (92.7%): 113/315 (35.9%) fullness values were corrected
cmag_354 (94.5%): 79/315 (25.1%) fullness values were corrected
cmag_355 (98.5%): 30/315 (9.5%) fullness values were corrected
cmag_356 (69.2%): 175/315 (55.6%) fullness values were corrected
cmag_357 (92.7%): 114/315 (36.2%) fullness values were corrected
cmag_358 (72.2%): 173/315 (54.9%) fullness values were corrected
cmag_359 (94.3%): 81/315 (25.7%) fullness values were corrected
cmag_360 (75.6%): 164/315 (52.1%) fullness values were corrected
cmag_361 (97.5%): 44/315 (14%) fullness values were corrected
cmag_362 (82.9%): 153/315 (48.6%) fullness values were corrected
cmag_363 (82.9%): 134/315 (42.5%) fullness values were corrected
cmag_364 (100%): 0/315 (0%) fullness values were corrected
cmag_365 (77%): 160/315 (50.8%) fullness values were corrected
cmag_366 (67.6%): 176/315 (55.9%) fullness values were corrected
cmag_367 (75.8%): 162/315 (51.4%) fullness values were corrected
cmag_368 (100%): 0/315 (0%) fullness values were corrected
cmag_369 (96.8%): 59/315 (18.7%) fullness values were corrected
cmag_370 (86.4%): 130/315 (41.3%) fullness values were corrected
cmag_371 (97.2%): 54/315 (17.1%) fullness values were corrected
cmag_372 (98.7%): 27/315 (8.6%) fullness values were corrected
cmag_373 (97.3%): 47/315 (14.9%) fullness values were corrected
cmag_374 (96.4%): 61/315 (19.4%) fullness values were corrected
cmag_375 (58.1%): 171/315 (54.3%) fullness values were corrected
cmag_376 (75.2%): 163/315 (51.7%) fullness values were corrected
cmag_377 (77.2%): 159/315 (50.5%) fullness values were corrected
cmag_378 (79.9%): 157/315 (49.8%) fullness values were corrected
cmag_379 (97.3%): 48/315 (15.2%) fullness values were corrected
cmag_380 (77.1%): 158/315 (50.2%) fullness values were corrected
cmag_381 (93.1%): 93/315 (29.5%) fullness values were corrected
cmag_382 (100%): 0/315 (0%) fullness values were corrected
cmag_383 (88.2%): 126/315 (40%) fullness values were corrected
cmag_384 (89.8%): 132/315 (41.9%) fullness values were corrected
cmag_385 (52.8%): 174/315 (55.2%) fullness values were corrected
cmag_386 (85.5%): 122/315 (38.7%) fullness values were corrected
cmag_387 (78%): 154/315 (48.9%) fullness values were corrected
cmag_388 (73.9%): 171/315 (54.3%) fullness values were corrected
cmag_389 (75.9%): 164/315 (52.1%) fullness values were corrected
cmag_390 (70.9%): 173/315 (54.9%) fullness values were corrected
cmag_391 (94.4%): 82/315 (26%) fullness values were corrected
cmag_392 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_393 (60.7%): 169/315 (53.7%) fullness values were corrected
cmag_394 (98%): 36/315 (11.4%) fullness values were corrected
cmag_395 (99.6%): 8/315 (2.5%) fullness values were corrected
cmag_396 (77.3%): 161/315 (51.1%) fullness values were corrected
cmag_397 (96%): 65/315 (20.6%) fullness values were corrected
cmag_398 (87.9%): 141/315 (44.8%) fullness values were corrected
cmag_399 (77%): 160/315 (50.8%) fullness values were corrected
cmag_400 (84.5%): 136/315 (43.2%) fullness values were corrected
cmag_401 (95.2%): 87/315 (27.6%) fullness values were corrected
cmag_402 (88%): 114/315 (36.2%) fullness values were corrected
cmag_403 (96%): 62/315 (19.7%) fullness values were corrected
cmag_404 (69.3%): 173/315 (54.9%) fullness values were corrected
cmag_405 (98%): 38/315 (12.1%) fullness values were corrected
cmag_406 (80.8%): 138/315 (43.8%) fullness values were corrected
cmag_407 (86.3%): 131/315 (41.6%) fullness values were corrected
cmag_408 (85.7%): 138/315 (43.8%) fullness values were corrected
cmag_409 (100%): 0/315 (0%) fullness values were corrected
cmag_410 (98%): 33/315 (10.5%) fullness values were corrected
cmag_411 (91.9%): 94/315 (29.8%) fullness values were corrected
cmag_412 (97%): 58/315 (18.4%) fullness values were corrected
cmag_413 (79.1%): 155/315 (49.2%) fullness values were corrected
cmag_414 (71.2%): 170/315 (54%) fullness values were corrected
cmag_415 (94.9%): 72/315 (22.9%) fullness values were corrected
cmag_416 (94.7%): 69/315 (21.9%) fullness values were corrected
cmag_417 (92.2%): 105/315 (33.3%) fullness values were corrected
cmag_418 (99.4%): 12/315 (3.8%) fullness values were corrected
cmag_419 (94.5%): 71/315 (22.5%) fullness values were corrected
cmag_420 (99.6%): 7/315 (2.2%) fullness values were corrected
cmag_421 (96.7%): 51/315 (16.2%) fullness values were corrected
cmag_422 (96.6%): 57/315 (18.1%) fullness values were corrected
cmag_423 (60%): 177/315 (56.2%) fullness values were corrected
cmag_424 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_425 (75.3%): 167/315 (53%) fullness values were corrected
cmag_426 (98.3%): 30/315 (9.5%) fullness values were corrected
cmag_427 (92.2%): 87/315 (27.6%) fullness values were corrected
cmag_428 (89.9%): 129/315 (41%) fullness values were corrected
cmag_429 (90.9%): 108/315 (34.3%) fullness values were corrected
cmag_431 (94%): 85/315 (27%) fullness values were corrected
cmag_432 (93%): 91/315 (28.9%) fullness values were corrected
cmag_433 (99.2%): 15/315 (4.8%) fullness values were corrected
cmag_434 (66.8%): 171/315 (54.3%) fullness values were corrected
cmag_435 (89.8%): 132/315 (41.9%) fullness values were corrected
cmag_436 (89.6%): 130/315 (41.3%) fullness values were corrected
cmag_437 (99.2%): 13/315 (4.1%) fullness values were corrected
cmag_438 (92.5%): 104/315 (33%) fullness values were corrected
cmag_439 (96.2%): 63/315 (20%) fullness values were corrected
cmag_440 (92%): 98/315 (31.1%) fullness values were corrected
cmag_441 (91%): 109/315 (34.6%) fullness values were corrected
cmag_442 (99.6%): 9/315 (2.9%) fullness values were corrected
cmag_443 (76.6%): 162/315 (51.4%) fullness values were corrected
cmag_444 (86.3%): 136/315 (43.2%) fullness values were corrected
cmag_445 (96%): 55/315 (17.5%) fullness values were corrected
cmag_446 (94.3%): 82/315 (26%) fullness values were corrected
cmag_447 (53.8%): 172/315 (54.6%) fullness values were corrected
cmag_448 (97.3%): 58/315 (18.4%) fullness values were corrected
cmag_449 (91.3%): 122/315 (38.7%) fullness values were corrected
cmag_450 (92.4%): 115/315 (36.5%) fullness values were corrected
cmag_451 (94.8%): 79/315 (25.1%) fullness values were corrected
cmag_452 (98.7%): 23/315 (7.3%) fullness values were corrected
cmag_453 (88.8%): 115/315 (36.5%) fullness values were corrected
cmag_454 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_455 (96.3%): 60/315 (19%) fullness values were corrected
cmag_456 (90.5%): 119/315 (37.8%) fullness values were corrected
cmag_457 (92.3%): 96/315 (30.5%) fullness values were corrected
cmag_458 (97.8%): 49/315 (15.6%) fullness values were corrected
cmag_459 (95.6%): 79/315 (25.1%) fullness values were corrected
cmag_460 (98.7%): 21/315 (6.7%) fullness values were corrected
cmag_461 (92.7%): 99/315 (31.4%) fullness values were corrected
cmag_462 (98.9%): 15/315 (4.8%) fullness values were corrected
cmag_463 (96.6%): 56/315 (17.8%) fullness values were corrected
cmag_464 (98.9%): 22/315 (7%) fullness values were corrected
cmag_465 (99.3%): 12/315 (3.8%) fullness values were corrected
cmag_466 (98%): 34/315 (10.8%) fullness values were corrected
cmag_467 (92.3%): 96/315 (30.5%) fullness values were corrected
cmag_468 (73.5%): 168/315 (53.3%) fullness values were corrected
cmag_469 (97.7%): 42/315 (13.3%) fullness values were corrected
cmag_470 (93.2%): 87/315 (27.6%) fullness values were corrected
cmag_471 (93.2%): 91/315 (28.9%) fullness values were corrected
cmag_472 (93.7%): 80/315 (25.4%) fullness values were corrected
cmag_473 (99.2%): 12/315 (3.8%) fullness values were corrected
cmag_474 (91.6%): 120/315 (38.1%) fullness values were corrected
cmag_475 (91.6%): 120/315 (38.1%) fullness values were corrected
cmag_476 (98.3%): 30/315 (9.5%) fullness values were corrected
cmag_477 (93%): 87/315 (27.6%) fullness values were corrected
cmag_478 (73.9%): 161/315 (51.1%) fullness values were corrected
cmag_479 (90.1%): 115/315 (36.5%) fullness values were corrected
cmag_480 (97.3%): 46/315 (14.6%) fullness values were corrected
cmag_481 (92.6%): 93/315 (29.5%) fullness values were corrected
cmag_482 (80.7%): 142/315 (45.1%) fullness values were corrected
cmag_483 (93%): 93/315 (29.5%) fullness values were corrected
cmag_484 (95.3%): 68/315 (21.6%) fullness values were corrected
cmag_485 (53.4%): 182/315 (57.8%) fullness values were corrected
cmag_486 (98.5%): 27/315 (8.6%) fullness values were corrected
cmag_487 (96.8%): 59/315 (18.7%) fullness values were corrected
cmag_488 (100%): 0/315 (0%) fullness values were corrected
cmag_489 (97.4%): 48/315 (15.2%) fullness values were corrected
cmag_490 (92%): 103/315 (32.7%) fullness values were corrected
cmag_491 (99%): 20/315 (6.3%) fullness values were corrected
cmag_492 (99.1%): 15/315 (4.8%) fullness values were corrected
cmag_493 (97.8%): 47/315 (14.9%) fullness values were corrected
cmag_494 (99.6%): 10/315 (3.2%) fullness values were corrected
cmag_495 (93.6%): 106/315 (33.7%) fullness values were corrected
cmag_496 (96.2%): 58/315 (18.4%) fullness values were corrected
cmag_497 (90.6%): 125/315 (39.7%) fullness values were corrected
cmag_498 (96.2%): 63/315 (20%) fullness values were corrected
cmag_499 (96.6%): 53/315 (16.8%) fullness values were corrected
cmag_500 (75.9%): 154/315 (48.9%) fullness values were corrected
cmag_501 (98.8%): 20/315 (6.3%) fullness values were corrected
cmag_502 (99.2%): 12/315 (3.8%) fullness values were corrected
cmag_503 (99.5%): 8/315 (2.5%) fullness values were corrected
cmag_504 (96.6%): 56/315 (17.8%) fullness values were corrected
cmag_505 (97.8%): 48/315 (15.2%) fullness values were corrected
cmag_506 (88.9%): 117/315 (37.1%) fullness values were corrected
cmag_507 (94.8%): 81/315 (25.7%) fullness values were corrected
cmag_508 (99.2%): 17/315 (5.4%) fullness values were corrected
cmag_509 (99.8%): 7/315 (2.2%) fullness values were corrected
cmag_510 (100%): 0/315 (0%) fullness values were corrected
cmag_511 (99.6%): 7/315 (2.2%) fullness values were corrected
cmag_512 (93.8%): 101/315 (32.1%) fullness values were corrected
cmag_513 (87%): 142/315 (45.1%) fullness values were corrected
cmag_514 (87.8%): 127/315 (40.3%) fullness values were corrected
cmag_515 (88.2%): 127/315 (40.3%) fullness values were corrected
cmag_516 (74.3%): 168/315 (53.3%) fullness values were corrected
cmag_517 (89.8%): 124/315 (39.4%) fullness values were corrected
cmag_518 (84.8%): 148/315 (47%) fullness values were corrected
cmag_519 (99.4%): 9/315 (2.9%) fullness values were corrected
cmag_520 (53.6%): 184/315 (58.4%) fullness values were corrected
cmag_521 (93.8%): 101/315 (32.1%) fullness values were corrected
cmag_522 (84.9%): 149/315 (47.3%) fullness values were corrected
cmag_523 (57.2%): 173/315 (54.9%) fullness values were corrected
cmag_524 (88.5%): 123/315 (39%) fullness values were corrected
cmag_525 (98.2%): 26/315 (8.3%) fullness values were corrected
cmag_526 (91.2%): 101/315 (32.1%) fullness values were corrected
cmag_527 (69.8%): 174/315 (55.2%) fullness values were corrected
cmag_528 (94.1%): 81/315 (25.7%) fullness values were corrected
cmag_529 (63.6%): 172/315 (54.6%) fullness values were corrected
cmag_530 (97%): 49/315 (15.6%) fullness values were corrected
cmag_531 (97.8%): 49/315 (15.6%) fullness values were corrected
cmag_532 (57.8%): 181/315 (57.5%) fullness values were corrected
cmag_533 (77.6%): 154/315 (48.9%) fullness values were corrected
cmag_534 (89.3%): 135/315 (42.9%) fullness values were corrected
cmag_535 (99.2%): 10/315 (3.2%) fullness values were corrected
cmag_536 (91.4%): 101/315 (32.1%) fullness values were corrected
cmag_537 (97.1%): 52/315 (16.5%) fullness values were corrected
cmag_538 (99.7%): 8/315 (2.5%) fullness values were corrected
cmag_539 (90%): 112/315 (35.6%) fullness values were corrected
cmag_540 (98%): 36/315 (11.4%) fullness values were corrected
cmag_541 (98%): 32/315 (10.2%) fullness values were corrected
cmag_542 (89%): 110/315 (34.9%) fullness values were corrected
cmag_543 (97%): 48/315 (15.2%) fullness values were corrected
cmag_544 (78%): 160/315 (50.8%) fullness values were corrected
cmag_545 (89.2%): 113/315 (35.9%) fullness values were corrected
cmag_546 (98%): 35/315 (11.1%) fullness values were corrected
cmag_547 (80.8%): 153/315 (48.6%) fullness values were corrected
cmag_548 (88%): 120/315 (38.1%) fullness values were corrected
cmag_549 (92.7%): 112/315 (35.6%) fullness values were corrected
cmag_550 (83.2%): 138/315 (43.8%) fullness values were corrected
cmag_551 (96.6%): 56/315 (17.8%) fullness values were corrected
cmag_552 (61.3%): 176/315 (55.9%) fullness values were corrected
cmag_553 (88.9%): 117/315 (37.1%) fullness values were corrected
cmag_555 (94.9%): 90/315 (28.6%) fullness values were corrected
cmag_556 (65.7%): 174/315 (55.2%) fullness values were corrected
cmag_557 (91.2%): 104/315 (33%) fullness values were corrected
cmag_558 (98.9%): 14/315 (4.4%) fullness values were corrected
cmag_559 (98%): 35/315 (11.1%) fullness values were corrected
cmag_560 (97.3%): 51/315 (16.2%) fullness values were corrected
cmag_561 (91.6%): 120/315 (38.1%) fullness values were corrected
cmag_562 (98.9%): 18/315 (5.7%) fullness values were corrected
cmag_563 (98.7%): 25/315 (7.9%) fullness values were corrected
cmag_564 (98%): 36/315 (11.4%) fullness values were corrected
cmag_565 (98.2%): 31/315 (9.8%) fullness values were corrected
cmag_566 (98.9%): 21/315 (6.7%) fullness values were corrected
cmag_567 (96.6%): 58/315 (18.4%) fullness values were corrected
cmag_568 (98.6%): 23/315 (7.3%) fullness values were corrected
cmag_569 (98%): 37/315 (11.7%) fullness values were corrected
cmag_570 (98.3%): 31/315 (9.8%) fullness values were corrected
cmag_571 (98.7%): 24/315 (7.6%) fullness values were corrected
cmag_572 (79.1%): 139/315 (44.1%) fullness values were corrected
cmag_573 (98.7%): 23/315 (7.3%) fullness values were corrected
cmag_574 (69.5%): 173/315 (54.9%) fullness values were corrected
cmag_575 (67%): 179/315 (56.8%) fullness values were corrected
cmag_576 (90.3%): 110/315 (34.9%) fullness values were corrected
cmag_577 (96.5%): 56/315 (17.8%) fullness values were corrected
cmag_578 (94.8%): 79/315 (25.1%) fullness values were corrected
cmag_579 (86%): 146/315 (46.3%) fullness values were corrected
cmag_580 (69.4%): 177/315 (56.2%) fullness values were corrected
cmag_581 (88.1%): 127/315 (40.3%) fullness values were corrected
cmag_582 (54.5%): 184/315 (58.4%) fullness values were corrected
cmag_583 (100%): 0/315 (0%) fullness values were corrected
cmag_584 (97.3%): 52/315 (16.5%) fullness values were corrected
cmag_585 (94.8%): 80/315 (25.4%) fullness values were corrected
cmag_586 (93%): 86/315 (27.3%) fullness values were corrected
cmag_587 (98.7%): 28/315 (8.9%) fullness values were corrected
cmag_588 (82.8%): 148/315 (47%) fullness values were corrected
cmag_589 (63.4%): 170/315 (54%) fullness values were corrected
cmag_590 (99.3%): 9/315 (2.9%) fullness values were corrected
cmag_591 (78.4%): 143/315 (45.4%) fullness values were corrected
cmag_592 (97.4%): 49/315 (15.6%) fullness values were corrected
cmag_593 (71.9%): 171/315 (54.3%) fullness values were corrected
cmag_594 (96.3%): 52/315 (16.5%) fullness values were corrected
cmag_595 (69.5%): 172/315 (54.6%) fullness values were corrected
cmag_596 (94.2%): 88/315 (27.9%) fullness values were corrected
cmag_597 (92.7%): 85/315 (27%) fullness values were corrected
cmag_598 (99.6%): 7/315 (2.2%) fullness values were corrected
cmag_599 (97.5%): 37/315 (11.7%) fullness values were corrected
cmag_600 (65.8%): 177/315 (56.2%) fullness values were corrected
cmag_601 (94.2%): 76/315 (24.1%) fullness values were corrected
cmag_602 (94%): 94/315 (29.8%) fullness values were corrected
cmag_603 (96.6%): 53/315 (16.8%) fullness values were corrected
cmag_604 (98.1%): 32/315 (10.2%) fullness values were corrected
cmag_605 (99.4%): 12/315 (3.8%) fullness values were corrected
cmag_606 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_607 (93.2%): 87/315 (27.6%) fullness values were corrected
cmag_608 (71.7%): 167/315 (53%) fullness values were corrected
cmag_609 (97.4%): 51/315 (16.2%) fullness values were corrected
cmag_610 (67.5%): 172/315 (54.6%) fullness values were corrected
cmag_611 (88.7%): 126/315 (40%) fullness values were corrected
cmag_612 (98%): 37/315 (11.7%) fullness values were corrected
cmag_613 (81.8%): 152/315 (48.3%) fullness values were corrected
cmag_614 (71.4%): 170/315 (54%) fullness values were corrected
cmag_615 (90.8%): 106/315 (33.7%) fullness values were corrected
cmag_616 (76.2%): 159/315 (50.5%) fullness values were corrected
cmag_617 (96.5%): 70/315 (22.2%) fullness values were corrected
cmag_618 (77.7%): 159/315 (50.5%) fullness values were corrected
cmag_619 (65.6%): 180/315 (57.1%) fullness values were corrected
cmag_620 (59.2%): 184/315 (58.4%) fullness values were corrected
cmag_621 (98.4%): 27/315 (8.6%) fullness values were corrected
cmag_622 (95.1%): 72/315 (22.9%) fullness values were corrected
cmag_623 (88.7%): 126/315 (40%) fullness values were corrected
cmag_624 (99.2%): 15/315 (4.8%) fullness values were corrected
cmag_625 (92%): 93/315 (29.5%) fullness values were corrected
cmag_626 (94.3%): 85/315 (27%) fullness values were corrected
cmag_627 (99.1%): 15/315 (4.8%) fullness values were corrected
cmag_628 (98.1%): 33/315 (10.5%) fullness values were corrected
cmag_629 (97.1%): 44/315 (14%) fullness values were corrected
cmag_630 (74.4%): 171/315 (54.3%) fullness values were corrected
cmag_631 (93.8%): 101/315 (32.1%) fullness values were corrected
cmag_632 (99.4%): 7/315 (2.2%) fullness values were corrected
cmag_633 (88.2%): 138/315 (43.8%) fullness values were corrected
cmag_634 (88.2%): 137/315 (43.5%) fullness values were corrected
cmag_635 (97.9%): 46/315 (14.6%) fullness values were corrected
cmag_636 (98.3%): 36/315 (11.4%) fullness values were corrected
cmag_637 (92.5%): 86/315 (27.3%) fullness values were corrected
cmag_638 (80.5%): 146/315 (46.3%) fullness values were corrected
cmag_639 (99.4%): 8/315 (2.5%) fullness values were corrected
cmag_640 (91.6%): 92/315 (29.2%) fullness values were corrected
cmag_641 (98.7%): 22/315 (7%) fullness values were corrected
cmag_642 (66.7%): 178/315 (56.5%) fullness values were corrected
cmag_643 (89.7%): 115/315 (36.5%) fullness values were corrected
cmag_644 (95.6%): 74/315 (23.5%) fullness values were corrected
cmag_645 (69.6%): 178/315 (56.5%) fullness values were corrected
cmag_646 (93.8%): 101/315 (32.1%) fullness values were corrected
cmag_647 (88.8%): 116/315 (36.8%) fullness values were corrected
cmag_648 (69.7%): 174/315 (55.2%) fullness values were corrected
cmag_649 (90.4%): 125/315 (39.7%) fullness values were corrected
cmag_650 (90.9%): 123/315 (39%) fullness values were corrected
cmag_651 (99.5%): 11/315 (3.5%) fullness values were corrected
cmag_652 (90.4%): 126/315 (40%) fullness values were corrected
cmag_653 (94.4%): 93/315 (29.5%) fullness values were corrected
cmag_654 (82.1%): 153/315 (48.6%) fullness values were corrected
cmag_655 (78.1%): 161/315 (51.1%) fullness values were corrected
cmag_656 (73.5%): 174/315 (55.2%) fullness values were corrected
cmag_657 (77.3%): 165/315 (52.4%) fullness values were corrected
cmag_658 (85.7%): 136/315 (43.2%) fullness values were corrected
cmag_659 (92.1%): 117/315 (37.1%) fullness values were corrected
cmag_660 (80%): 156/315 (49.5%) fullness values were corrected
cmag_661 (88.8%): 136/315 (43.2%) fullness values were corrected
cmag_662 (87.7%): 142/315 (45.1%) fullness values were corrected
cmag_663 (96.4%): 63/315 (20%) fullness values were corrected
cmag_664 (84%): 143/315 (45.4%) fullness values were corrected
cmag_665 (96.3%): 60/315 (19%) fullness values were corrected
cmag_666 (67.5%): 176/315 (55.9%) fullness values were corrected
cmag_667 (92.1%): 100/315 (31.7%) fullness values were corrected
cmag_668 (92.8%): 92/315 (29.2%) fullness values were corrected
cmag_669 (82.6%): 126/315 (40%) fullness values were corrected
cmag_670 (77.3%): 164/315 (52.1%) fullness values were corrected
cmag_671 (76.5%): 167/315 (53%) fullness values were corrected
cmag_672 (93.8%): 82/315 (26%) fullness values were corrected
cmag_673 (66.6%): 166/315 (52.7%) fullness values were corrected
cmag_674 (93.3%): 91/315 (28.9%) fullness values were corrected
cmag_675 (92.9%): 86/315 (27.3%) fullness values were corrected
cmag_676 (96.6%): 53/315 (16.8%) fullness values were corrected
cmag_677 (100%): 0/315 (0%) fullness values were corrected
cmag_678 (94.8%): 79/315 (25.1%) fullness values were corrected
cmag_679 (89.4%): 128/315 (40.6%) fullness values were corrected
cmag_680 (89.5%): 120/315 (38.1%) fullness values were corrected
cmag_681 (76.4%): 158/315 (50.2%) fullness values were corrected
cmag_682 (96.6%): 58/315 (18.4%) fullness values were corrected
cmag_683 (94%): 85/315 (27%) fullness values were corrected
cmag_684 (100%): 0/315 (0%) fullness values were corrected
cmag_685 (91.9%): 100/315 (31.7%) fullness values were corrected
cmag_686 (90.8%): 116/315 (36.8%) fullness values were corrected
cmag_687 (64.7%): 176/315 (55.9%) fullness values were corrected
cmag_688 (96.4%): 59/315 (18.7%) fullness values were corrected
cmag_689 (79.5%): 157/315 (49.8%) fullness values were corrected
cmag_690 (86.8%): 132/315 (41.9%) fullness values were corrected
cmag_691 (91.6%): 107/315 (34%) fullness values were corrected
cmag_692 (89.2%): 135/315 (42.9%) fullness values were corrected
cmag_693 (93.8%): 94/315 (29.8%) fullness values were corrected
cmag_694 (94%): 86/315 (27.3%) fullness values were corrected
cmag_695 (94.6%): 84/315 (26.7%) fullness values were corrected
cmag_696 (93.2%): 93/315 (29.5%) fullness values were corrected
cmag_697 (89.7%): 116/315 (36.8%) fullness values were corrected
cmag_698 (97.6%): 51/315 (16.2%) fullness values were corrected
cmag_699 (75%): 153/315 (48.6%) fullness values were corrected
cmag_700 (98%): 36/315 (11.4%) fullness values were corrected
cmag_701 (94.2%): 81/315 (25.7%) fullness values were corrected
cmag_702 (95.3%): 76/315 (24.1%) fullness values were corrected
cmag_703 (96.3%): 54/315 (17.1%) fullness values were corrected
cmag_704 (97.4%): 51/315 (16.2%) fullness values were corrected
cmag_705 (95.5%): 69/315 (21.9%) fullness values were corrected
cmag_706 (95.3%): 64/315 (20.3%) fullness values were corrected
cmag_707 (94.3%): 76/315 (24.1%) fullness values were corrected
cmag_708 (95.2%): 68/315 (21.6%) fullness values were corrected
cmag_709 (98%): 34/315 (10.8%) fullness values were corrected
cmag_710 (96.4%): 55/315 (17.5%) fullness values were corrected
cmag_711 (91.4%): 101/315 (32.1%) fullness values were corrected
cmag_712 (98.3%): 30/315 (9.5%) fullness values were corrected
cmag_713 (98.7%): 25/315 (7.9%) fullness values were corrected
cmag_714 (97.3%): 53/315 (16.8%) fullness values were corrected
cmag_715 (96.8%): 54/315 (17.1%) fullness values were corrected
cmag_716 (86.1%): 146/315 (46.3%) fullness values were corrected
cmag_717 (90.4%): 104/315 (33%) fullness values were corrected
cmag_718 (66.7%): 171/315 (54.3%) fullness values were corrected
cmag_719 (99.5%): 8/315 (2.5%) fullness values were corrected
cmag_720 (95.6%): 74/315 (23.5%) fullness values were corrected
cmag_721 (92.7%): 91/315 (28.9%) fullness values were corrected
cmag_722 (92.6%): 97/315 (30.8%) fullness values were corrected
cmag_723 (97.3%): 50/315 (15.9%) fullness values were corrected
cmag_724 (93.7%): 80/315 (25.4%) fullness values were corrected
cmag_725 (89.9%): 111/315 (35.2%) fullness values were corrected
cmag_726 (75.8%): 162/315 (51.4%) fullness values were corrected
cmag_727 (95.3%): 78/315 (24.8%) fullness values were corrected
cmag_728 (98%): 36/315 (11.4%) fullness values were corrected
cmag_729 (98.7%): 24/315 (7.6%) fullness values were corrected
cmag_730 (84.8%): 149/315 (47.3%) fullness values were corrected
cmag_731 (98.7%): 26/315 (8.3%) fullness values were corrected
cmag_732 (96.3%): 56/315 (17.8%) fullness values were corrected
cmag_733 (100%): 0/315 (0%) fullness values were corrected
cmag_734 (93.3%): 92/315 (29.2%) fullness values were corrected
cmag_735 (54.7%): 181/315 (57.5%) fullness values were corrected
cmag_736 (98.2%): 29/315 (9.2%) fullness values were corrected
cmag_737 (98%): 32/315 (10.2%) fullness values were corrected
cmag_738 (98.7%): 19/315 (6%) fullness values were corrected
cmag_739 (92.7%): 99/315 (31.4%) fullness values were corrected
cmag_740 (95.3%): 76/315 (24.1%) fullness values were corrected
cmag_741 (71.9%): 176/315 (55.9%) fullness values were corrected
cmag_742 (93.4%): 81/315 (25.7%) fullness values were corrected
cmag_743 (96.4%): 57/315 (18.1%) fullness values were corrected
cmag_744 (69.4%): 176/315 (55.9%) fullness values were corrected
cmag_745 (73.2%): 154/315 (48.9%) fullness values were corrected
cmag_746 (98.7%): 21/315 (6.7%) fullness values were corrected
cmag_747 (89%): 135/315 (42.9%) fullness values were corrected
cmag_748 (96.6%): 56/315 (17.8%) fullness values were corrected
cmag_749 (92.4%): 95/315 (30.2%) fullness values were corrected
cmag_750 (100%): 0/315 (0%) fullness values were corrected
cmag_751 (89.4%): 112/315 (35.6%) fullness values were corrected
cmag_752 (91%): 100/315 (31.7%) fullness values were corrected
cmag_753 (70.6%): 172/315 (54.6%) fullness values were corrected
cmag_754 (98.2%): 31/315 (9.8%) fullness values were corrected
cmag_755 (89.7%): 110/315 (34.9%) fullness values were corrected
cmag_756 (90.7%): 125/315 (39.7%) fullness values were corrected
cmag_757 (76.7%): 162/315 (51.4%) fullness values were corrected
cmag_758 (59.7%): 180/315 (57.1%) fullness values were corrected
cmag_759 (96%): 62/315 (19.7%) fullness values were corrected
cmag_760 (78.7%): 155/315 (49.2%) fullness values were corrected
cmag_761 (92.7%): 114/315 (36.2%) fullness values were corrected
cmag_762 (92.7%): 113/315 (35.9%) fullness values were corrected
cmag_763 (98.9%): 22/315 (7%) fullness values were corrected
cmag_764 (98.5%): 26/315 (8.3%) fullness values were corrected
cmag_765 (92.7%): 113/315 (35.9%) fullness values were corrected
cmag_766 (77.3%): 146/315 (46.3%) fullness values were corrected
cmag_767 (93.3%): 108/315 (34.3%) fullness values were corrected
cmag_768 (70.2%): 163/315 (51.7%) fullness values were corrected
cmag_769 (93%): 98/315 (31.1%) fullness values were corrected
cmag_770 (71.2%): 174/315 (55.2%) fullness values were corrected
cmag_771 (89.7%): 123/315 (39%) fullness values were corrected
cmag_772 (96.2%): 62/315 (19.7%) fullness values were corrected
cmag_773 (69.9%): 173/315 (54.9%) fullness values were corrected
cmag_774 (96%): 64/315 (20.3%) fullness values were corrected
cmag_775 (94.8%): 81/315 (25.7%) fullness values were corrected
cmag_776 (65.8%): 175/315 (55.6%) fullness values were corrected
cmag_777 (95.6%): 66/315 (21%) fullness values were corrected
cmag_778 (98.7%): 23/315 (7.3%) fullness values were corrected
cmag_779 (77.2%): 164/315 (52.1%) fullness values were corrected
cmag_780 (99%): 20/315 (6.3%) fullness values were corrected
cmag_781 (91.8%): 120/315 (38.1%) fullness values were corrected
cmag_782 (99.7%): 9/315 (2.9%) fullness values were corrected
cmag_783 (89.8%): 116/315 (36.8%) fullness values were corrected
cmag_784 (98%): 38/315 (12.1%) fullness values were corrected
cmag_785 (94.6%): 80/315 (25.4%) fullness values were corrected
cmag_786 (91%): 111/315 (35.2%) fullness values were corrected
cmag_787 (82.6%): 153/315 (48.6%) fullness values were corrected
cmag_788 (92.8%): 95/315 (30.2%) fullness values were corrected
cmag_789 (97.6%): 41/315 (13%) fullness values were corrected
cmag_790 (95.1%): 70/315 (22.2%) fullness values were corrected
cmag_791 (99.4%): 12/315 (3.8%) fullness values were corrected
cmag_792 (65.8%): 173/315 (54.9%) fullness values were corrected
cmag_793 (93.2%): 86/315 (27.3%) fullness values were corrected
cmag_794 (98.3%): 29/315 (9.2%) fullness values were corrected
cmag_795 (98%): 35/315 (11.1%) fullness values were corrected
cmag_796 (86.7%): 141/315 (44.8%) fullness values were corrected
cmag_797 (98.4%): 29/315 (9.2%) fullness values were corrected
cmag_798 (96.3%): 58/315 (18.4%) fullness values were corrected
cmag_799 (91.7%): 107/315 (34%) fullness values were corrected
cmag_800 (91.6%): 104/315 (33%) fullness values were corrected
cmag_801 (97.3%): 50/315 (15.9%) fullness values were corrected
cmag_802 (97.5%): 45/315 (14.3%) fullness values were corrected
cmag_803 (95.6%): 75/315 (23.8%) fullness values were corrected
cmag_804 (69.6%): 171/315 (54.3%) fullness values were corrected
cmag_805 (92.5%): 98/315 (31.1%) fullness values were corrected
cmag_806 (92.7%): 100/315 (31.7%) fullness values were corrected
cmag_807 (74.1%): 170/315 (54%) fullness values were corrected
cmag_808 (91%): 122/315 (38.7%) fullness values were corrected
cmag_809 (94.6%): 71/315 (22.5%) fullness values were corrected
cmag_810 (74.3%): 165/315 (52.4%) fullness values were corrected
cmag_811 (55.9%): 183/315 (58.1%) fullness values were corrected
cmag_812 (76.7%): 161/315 (51.1%) fullness values were corrected
cmag_813 (94.8%): 78/315 (24.8%) fullness values were corrected
cmag_814 (98.7%): 23/315 (7.3%) fullness values were corrected
cmag_815 (96.8%): 63/315 (20%) fullness values were corrected
cmag_816 (99.3%): 11/315 (3.5%) fullness values were corrected
cmag_817 (68.6%): 172/315 (54.6%) fullness values were corrected
cmag_818 (87.1%): 146/315 (46.3%) fullness values were corrected
cmag_819 (93%): 110/315 (34.9%) fullness values were corrected
cmag_820 (65.1%): 180/315 (57.1%) fullness values were corrected
cmag_821 (93.8%): 101/315 (32.1%) fullness values were corrected
cmag_822 (88.6%): 121/315 (38.4%) fullness values were corrected
cmag_823 (98.7%): 24/315 (7.6%) fullness values were corrected
cmag_824 (99.4%): 11/315 (3.5%) fullness values were corrected
cmag_825 (83.4%): 121/315 (38.4%) fullness values were corrected16.5 compare MCI values without and with correction
# Load data
load("data/correction_files.Rdata")
# calculate average MCI by MAG
# a) without correction
overall_mci <-
gifts_elements %>%
as.data.frame() %>%
rownames_to_column(var = "genome") %>%
rowwise() %>%
mutate(mean_MCI = mean(c_across(B0101:S0301))) %>%
select(genome, mean_MCI) %>%
left_join(genome_stats, by = "genome")%>%
mutate(mag_length = mag_length / 1000000) %>%
left_join(genome_taxonomy, by = "genome")
# b) Applying correction
overall_mci_corrected <-
gifts_elements_corrected %>%
as.data.frame() %>%
rownames_to_column(var = "genome") %>%
rowwise() %>%
mutate(mean_MCI = mean(c_across(B0101:S0301))) %>%
select(genome, mean_MCI) %>%
left_join(genome_stats, by = "genome") %>%
mutate(mag_length = mag_length / 1000000) %>%
left_join(genome_taxonomy, by = "genome")16.6 Spearman correlation
# a) without correction
cor(overall_mci$mean_MCI, overall_mci$completeness_score, method = "spearman")[1] 0.6310837# b) Applying correction
cor(overall_mci_corrected$mean_MCI, overall_mci_corrected$completeness_score, method = "spearman")[1] 0.22055316.7 Comparing average MCI with genome completeness
# a) Without correction
overall_mci %>%
ggplot(aes(x = completeness_score, y = mean_MCI, color = order)) +
geom_point(size = 2.5) +
xlim(50,100) + ylim(0, 0.6) +
scale_color_manual(values = order_colors) +
theme_bw() +
theme(legend.position = 'none') +
xlab("Completeness score") + ylab("Mean MCI") +
ggtitle("Without correction")
# b) Applying correction
overall_mci_corrected %>%
ggplot(aes(x = completeness_score, y = mean_MCI, color = order)) +
geom_point(size = 2.5) +
xlim(50,100) + ylim(0, 0.6) +
scale_color_manual(values = order_colors) +
xlab("Completeness score") + ylab("Mean MCI") +
theme_bw() +
theme(legend.position = 'none') +
ggtitle("Applying correction")
16.9 Spearman correlation
# a) Without correction
cor(reduced_genomes$mean_MCI, reduced_genomes$completeness_score, method = "spearman")[1] 0.5533165# b) Applying correction
cor(reduced_genomes_corrected$mean_MCI, reduced_genomes_corrected$completeness_score, method = "spearman")[1] -0.93274616.10 Illustrating correlation between average MCI and completeness
# a) Without correction
reduced_genomes %>%
ggplot(aes(x = completeness_score, y = mean_MCI, color = order)) +
geom_point(size = 2.5) +
xlim(50,100) + ylim(0, 0.6) +
scale_color_manual(values = order_colors) +
theme_bw() +
theme(legend.position = 'none') +
xlab("Completeness score") + ylab("Mean MCI") +
ggtitle("Without correction")
# b) Applying correction
reduced_genomes_corrected %>%
ggplot(aes(x = completeness_score, y = mean_MCI, color = order)) +
geom_point(size = 2.5) +
xlim(50,100) + ylim(0, 0.6) +
scale_color_manual(values = order_colors) +
xlab("Completeness score") + ylab("Mean MCI") +
theme_bw() +
theme(legend.position = 'none') +
ggtitle("Applying correction")
16.11 Testing differences at community-weighted MCI
# Load community-weighted MCI without correction
load("data/mci_com.Rdata")
funcs_com %>%
as.data.frame() %>%
rownames_to_column('animal_code') %>%
rowwise() %>%
mutate(overall = mean(c_across(B01:D09))) %>%
select(animal_code, overall) %>%
left_join(chicken_metadata %>%
select(animal_code, sampling_time),
by = 'animal_code') %>%
ggplot(aes(x = sampling_time,
y = overall,
group = sampling_time)) +
geom_jitter(aes_string(colour = 'sampling_time'), size = 0.3, width = 0.2, alpha = 0.6) +
geom_boxplot(aes_string(fill = 'sampling_time'), width = 0.4, alpha = 0.5, outlier.color = NA) +
scale_fill_manual(values = c('#E69F00', '#CC6677', '#56B4E9')) +
scale_color_manual(values = c('#E69F00', '#CC6677', '#56B4E9')) +
theme_bw() +
theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.x = element_text(size = 8),
axis.text.y = element_text(size = 8),
legend.position = 'none') +
ggtitle("Without correction")
# Calculate community-weighted MCI applying correction
funcs_com_corrected <- to.community(gifts_functions_corrected, total, GIFT_db2)
funcs_com_corrected %>%
as.data.frame() %>%
rownames_to_column('animal_code') %>%
rowwise() %>%
mutate(overall = mean(c_across(B01:D09))) %>%
select(animal_code, overall) %>%
left_join(chicken_metadata %>%
select(animal_code, sampling_time),
by = 'animal_code') %>%
ggplot(aes(x = sampling_time,
y = overall,
group = sampling_time)) +
geom_jitter(aes_string(colour = 'sampling_time'), size = 0.3, width = 0.2, alpha = 0.6) +
geom_boxplot(aes_string(fill = 'sampling_time'), width = 0.4, alpha = 0.5, outlier.color = NA) +
scale_fill_manual(values = c('#E69F00', '#CC6677', '#56B4E9')) +
scale_color_manual(values = c('#E69F00', '#CC6677', '#56B4E9')) +
theme_bw() +
theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.x = element_text(size = 8),
axis.text.y = element_text(size = 8),
legend.position = 'none') +
ggtitle("Applying correction")