Table 2 |
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|
Genotyping results obtained from exome capture data produced in this study |
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|
Percentage |
Variant |
Heterozygous |
Homozygous |
Transition/transversion |
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|
|
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|
Sample |
called |
number |
Syn. |
Non-syn. |
Syn. |
Non-syn. |
ratio |
|
|
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|
CEU-D-NM-LN1 |
80.85 |
12,994 |
3,547 |
4,359 |
2,828 |
2,260 |
3.48 |
|
CEU-F-NM-LN1 |
79.68 |
12,501 |
3,413 |
4,182 |
2,726 |
2,180 |
3.45 |
|
CEU-M-NM-LN1 |
84.93 |
13,934 |
3,848 |
4,668 |
3,019 |
2,399 |
3.35 |
|
YRI-D-AG-LN1 |
86.38 |
17,214 |
5,161 |
6,082 |
3,266 |
2,705 |
3.44 |
|
YRI-D-AG-LN12 |
91.48 |
18,803 |
5,608 |
6,728 |
3,530 |
2,937 |
3.43 |
|
YRI-D-AG-LN123 |
93.33 |
19,468 |
5,804 |
6,974 |
3,665 |
3,025 |
3.41 |
|
YRI-D-AG-LN1234 |
94.17 |
19,719 |
5,869 |
7,061 |
3,708 |
3,081 |
3.41 |
|
YRI-D-AG-LN2 |
86.09 |
17,145 |
5,097 |
6,110 |
3,236 |
2,702 |
3.47 |
|
YRI-D-AG-LN3 |
86.04 |
17,161 |
5,127 |
6,091 |
3,238 |
2,705 |
3.47 |
|
YRI-D-AG-LN4 |
84.99 |
16,708 |
4,976 |
5,909 |
3,176 |
2,647 |
3.45 |
|
YRI-D-NM-LN1 |
84.27 |
17,146 |
5,014 |
6,273 |
3,272 |
2,587 |
3.47 |
|
YRI-D-NM-LN12 |
86.15 |
17,864 |
5,258 |
6,530 |
3,378 |
2,698 |
3.38 |
|
YRI-D-NM-LN123 |
86.71 |
18,081 |
5,328 |
6,608 |
3,405 |
2,740 |
3.35 |
|
YRI-D-NM-LN1234 |
87.01 |
18,208 |
5,376 |
6,642 |
3,426 |
2,764 |
3.33 |
|
YRI-D-NM-LN2 |
84.17 |
17,341 |
5,080 |
6,359 |
3,292 |
2,610 |
3.44 |
|
YRI-D-NM-LN3 |
84.06 |
17,328 |
5,101 |
6,336 |
3,289 |
2,602 |
3.40 |
|
YRI-D-NM-LN4 |
83.92 |
17,213 |
5,033 |
6,319 |
3,268 |
2,593 |
3.44 |
|
YRI-F-NM-LN1 |
85.26 |
17,389 |
5,006 |
6,217 |
3,446 |
2,720 |
3.38 |
|
YRI-F-NM-LN12 |
86.57 |
17,820 |
5,128 |
6,366 |
3,517 |
2,809 |
3.35 |
|
YRI-F-NM-LN2 |
84.62 |
17,294 |
4,966 |
6,194 |
3,419 |
2,715 |
3.41 |
|
YRI-M-AG-LN1 |
86.20 |
16,991 |
5,101 |
5,974 |
3,226 |
2,690 |
3.39 |
|
YRI-M-AG-LN12 |
90.97 |
18,452 |
5,523 |
6,539 |
3,501 |
2,889 |
3.36 |
|
YRI-M-AG-LN123 |
92.89 |
19,086 |
5,685 |
6,798 |
3,606 |
2,997 |
3.35 |
|
YRI-M-AG-LN1234 |
93.97 |
19,423 |
5,799 |
6,917 |
3,669 |
3,038 |
3.33 |
|
YRI-M-AG-LN2 |
83.48 |
16,095 |
4,859 |
5,619 |
3,059 |
2,558 |
3.37 |
|
YRI-M-AG-LN3 |
84.59 |
16,472 |
4,933 |
5,772 |
3,136 |
2,631 |
3.42 |
|
YRI-M-AG-LN4 |
85.95 |
16,832 |
5,032 |
5,897 |
3,215 |
2,688 |
3.38 |
|
YRI-M-NM-LN1 |
84.85 |
17,195 |
5,028 |
6,259 |
3,278 |
2,630 |
3.35 |
|
YRI-M-NM-LN12 |
86.33 |
17,742 |
5,219 |
6,458 |
3,358 |
2,707 |
3.29 |
|
YRI-M-NM-LN123 |
86.81 |
17,936 |
5,283 |
6,516 |
3,392 |
2,745 |
3.26 |
|
YRI-M-NM-LN1234 |
87.06 |
18,034 |
5,306 |
6,553 |
3,414 |
2,761 |
3.24 |
|
YRI-M-NM-LN2 |
84.52 |
17,222 |
5,043 |
6,271 |
3,285 |
2,623 |
3.35 |
|
YRI-M-NM-LN3 |
84.53 |
17,205 |
5,031 |
6,265 |
3,274 |
2,635 |
3.38 |
|
YRI-M-NM-LN4 |
84.40 |
17,197 |
5,045 |
6,252 |
3,268 |
2,632 |
3.36 |
|
|
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|
Sequencing lanes were arbitrarily numbered from 1 through 4, irrespective of the actual lane on the Illumina flowcell the data were generated from. Lane data merges are represented by the digits after LN (lane), with LN1 representing the data from a single lane, LN12 representing the data from the two lanes LN1 and LN2, LN123 representing the data from the three lanes LN1, LN2, and LN3, and so forth. Genotypes were assigned based on consensus quality of 50 or above [15], and the proportion of the CCDS target bases genotyped using this filter is indicated for each dataset. The extent of CCDS coverage had a direct influence on the extent of genotyping we were able to carry out with each dataset. It is also apparent that increasing raw sequence data, obtained by lane merges in this study, results in increases in the number of genotypic variants detected. The YRI individuals were found to have a greater number of variants than the CEU individuals, which has also been determined in other studies [13,18]. Syn., synonymous. |
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|
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97 |
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