Table A3.
Comparison of SNPs summaries in different genomes.
| NECS |
Watson | Venter | Complete genomics |
AK1 | YH | Illumina |
1000 Genomes |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Male >111 | Female >113 | NA07022 (CEU/M) | NA20431 (PG/M) | NA19240 (YRI/F) | NA 18507 (YRI/m) | CEU trio | YRI trio | |||||
| Ti/Tv (in dbSNP) | 2.11 | 2.07 | 2.01 | 2.04 | 2.17 | 2.19 | 2.13 | 2.07 | 2.01 | 2.06 | 2.07 | 2.09 |
| Ti/Tv (only 1000 genomes) | 2.33 | 2.27 | ||||||||||
| Ti/Tv (Novel) | 2.07 | 2.13 | 1.94 | 2.02 | ||||||||
| het/homo (in dbSNP) | 1.41 | 1.24 | 1.30 | 1.2 | 1.64 | 1.72 | 2.01 | 1.57 | 1.27 | 1.75 | ||
| het/homo (only 1000 genomes) | 14.57 | 7.12 | ||||||||||
| het/homo (Novel) | 6.28 | 9.16 | 12.3 | 27.48 | 13.73 | |||||||
| Mean mapped depth | 41.64 | 35.05 | 7.40 | 7.5 | 87 | 45 | 63 | 29 | 36 | 41 | 43 | 40 |
| Mean mapped depth (only 1000 genomes) | 35.51 | 30.02 | ||||||||||
| Mean mapped depth (Novel) | 37.93 | 34.08 | ||||||||||
| CGI | http://www.completegenomics.com/sequence-data/data-summary/ | |||||||||||
| Watson/Venter/AK1/YH | http://www.nature.com/nature/journal/v460/n7258/full/nature08211.html | |||||||||||
| Illumina | http://www.nature.com/nature/journal/v456/n7218/full/nature07517.html | |||||||||||
| 1000 Genomes | http://www.nature.com/nature/journal/v467/n7319/full/nature09534.html | |||||||||||
| Venter | http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050254 | |||||||||||
The comparative values were taken from published references noted in the table. These references did not report the summaries stratified by whether they were novel and/or reported only in 1000 genomes database.