Table 2 |
|||||||||
|
Summary of genetic variants identified through exome sequencing |
|||||||||
|
Sample |
ND02537 |
ND02538 |
ND02539 |
ND02540 |
Average |
||||
|
|
|||||||||
|
DNA source |
PBMC |
LCL |
PBMC |
LCL |
PBMC |
LCL |
PBMC |
LCL |
|
|
|
|||||||||
|
Total Variants: SNPs and Indels (novel) |
20238 (1354) |
20366 (1380) |
17770 (1222) |
17912 (1242) |
19306 (1412) |
19317 (1449) |
19895 (1872) |
20032 (1518) |
19354 (1431) |
|
|
|||||||||
|
Shared between 2-paired samples |
19932 |
17456 |
18879 |
19509 |
18944 |
||||
|
|
|||||||||
|
Discordant variants |
306 |
434 |
274 |
456 |
427 |
438 |
386 |
542 |
407 |
|
|
|||||||||
|
|
|||||||||
|
Total concordance rate |
96.29% |
95.82% |
95.42% |
95.24% |
95.69% |
||||
|
|
|||||||||
|
Total SNPs (novel) |
18660 (485) |
18794 (491) |
16184 (388) |
16316 (401) |
17531 (467) |
17597 (471) |
18079 (617) |
18216 (574) |
17672 (486) |
|
|
|||||||||
|
Shared between 2- paired samples |
18433 |
15963 |
17214 |
17806 |
17354 |
||||
|
|
|||||||||
|
Discordant SNPs |
227 |
361 |
221 |
353 |
317 |
383 |
273 |
410 |
318 |
|
|
|||||||||
|
SNP concordance rate |
96.81% |
96.40% |
95.93% |
96.16% |
96.33% |
||||
|
|
|||||||||
|
|
|||||||||
|
Total Indels (novel) |
1578 (869) |
1572 (889) |
1586 (834) |
1596 (841) |
1775 (945) |
1720 (978) |
1816 (955) |
1835 (944) |
1684 (906) |
|
|
|||||||||
|
Shared between 2-paired samples |
1499 |
1493 |
1665 |
1703 |
1571 |
||||
|
|
|||||||||
|
Discordant indels |
79 |
73 |
53 |
103 |
110 |
55 |
113 |
132 |
90 |
|
|
|||||||||
|
Indel Concordance rate |
89.86% |
89.55% |
90.09% |
85.61% |
88.78% |
||||
|
|
|||||||||
|
Londin et al. BMC Genomics 2011 12:464 doi:10.1186/1471-2164-12-464 |
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