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.