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Table 1 Quality metrics of the sequenced genomes

From: In depth comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing

 

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

  1. This table also lists information on the number and kind of indels identified per genome, but does not contain data on structural variances.
  2. Gb: gigabase, SNP: single nucleotide polymorphism, INS: insertion, DEL: deletion, SUB: substitution, (Non)syn: (non-)synonymous.