A total of 2,474,648 SNPs are found from the donor's genome as defined by Maq X and additional filteration (Table X), which criteria were decribed in Supplementary Information. Evaluatation of the quantity and quality of the detected SNPs were undergone by comparing the overlap and uniqueness of these variants with the three available indiviidual genomes (James D. Watson, J. Craig Venter, and BGI YH), and dbSNP (v129) and Hapmap (ver X) (Figure X).
Of the total SNPs, x,xxx,xxx variants were detected in the Venter genome, x,xxx,xxx SNPs in the Watson genome, and x,xxx,xxx in the BGI YH genome (Figure Xa), and 1,574,921 variants (1,363,868 as validated and 210,053 as non-validated) were presented in dbSNP and x,xxx,xxx in Hapmap (Figure Xb).
The remaining 899,727 SNPs (36%) in total SNPs were novel.
We found that 1,390,446 of the KSJ SNPs were show dbSNP as validated SNPs, and 220,564 were show as non-validated SNPs. The remaining 50% (1623913) of total SNPs were novel.
| Heterozygote Reads >= 1 | Heterozygote Reads >= 2 | Direffence | |
| Total SNPs |
3,234,923 (has 1480 error clmns) 3,200,113 (real data) |
2,474,648 |
760,275 |
| Validated dbSNP | 1,390,446 | 1,364,868 | 25,578 |
| Unvalidated dbSNP | 220,564 | 210,053 | 10,511 |
| Total of dbSNP |
1,598,254 |
1,574,921 |
|
| Novel SNPs |
1,623,913 |
899,727 |
724,186 |
** a number of ref read + other allele != total read was 220,152, and incomplete data with 8 columns 1,480.
Table X. Detected SNPs
| Detected SNPs | |
| Validated dbSNP | 1390446 |
| Unvalidated dbSNP | 220564 |
| Novel SNPs | 1623913 |
Detected SNPs (Total Reads >= 5, Heterozygote Reads >=2)
| Detected SNPs | |
| Validated dbSNP | 1364868 |
| Unvalidated dbSNP | 210053 |
| Novel SNPs | 899727 |
Detail information
- TOTAL SNP : 2474648
- KNOWN SNP : 1573571 (BGI) / 1574921(dbSNP 129) : +1350
- NOVEL SNP : 901077 (BGI) / 899727 (dbSNP 129) : -1350
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- CALL ERROR SNP : 1480
- FILTER OUT SNP : 758795 (TOTAL READs : < 5, HETERO READs : < 2)
Maq 를 통해 SNP 뽑을 때, Consensus quaility, Adjust quaility, Read수는 3개를 사용했을때 2,400,000 나왔다.
Read deapth 를 어떻게 할꺼냐? 8개 or 10개
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