Table 1

Quality metrics of the sequenced genomes
genomic cell line
Gender male male
Gross mapping yield (Gb) 238.95 217.33
SNP Transitions/transversions 2.14076 2.1468
SNP het/hom ratio 1.582496107 1.571157051
INS het/hom ratio 1.344223031 1.289809921
DEL het/hom ratio 1.663654705 1.654600015
SUB het/hom ratio 1.715782613 1.713757678
SNP total count 3346813 3271797
INS total count 187392 170265
DEL total count 204807 186626
SUB total count 71344 66370
SNP novel rate 0.0487541 0.0472266
INS novel rate 0.189213 0.17794
DEL novel rate 0.239469 0.235096
SUB novel rate 0.309865 0.295857
Fully called genome fraction 0.967831529 0.961877785
Partially called genome fraction 0.004574129 0.006604011
No-called genome fraction 0.027594342 0.031518204
Synonymous SNP loci 9778 9387
Missense SNP loci 9329 8935
Nonsense SNP loci 90 89
Nonstop SNP loci 13 13
Frame-shifting INS loci 121 110
Frame-shifting DEL loci 108 100
Frame-shifting SUB loci 17 13
Frame-preserving INS loci 113 101
Frame-preserving DEL loci 107 91
Frame-preserving SUB loci 258 227
Frame-shifting/preserving ratio 0.514644351 0.53221957
Nonsyn/syn SNP ratio 0.954080589 0.951848301
Insertion/deletions ratio 0.914968727 0.912332687
Ins + del/SNP ratio 0.117185812 0.109081034
Coding insertion/deletions ratio 1.060465116 1.078534031
Coding SNP/all SNP ratio 0.00626387 0.006151054
Coding (ins + del)/all (ins + del) ratio 0.001129529 0.001112384

This table also lists information on the number and kind of indels identified per genome, but does not contain data on structural variances.

Gb: gigabase, SNP: single nucleotide polymorphism, INS: insertion, DEL: deletion, SUB: substitution, (Non)syn: (non-)synonymous.

Nickles et al.

Nickles et al. BMC Genomics 2012 13:477   doi:10.1186/1471-2164-13-477

Open Data