TABLE 1 .
Intragenomic SNPs within the sequenced SS1 populationa
| Position | Base 1 (no. of reads) | Base 2 (no. of reads) | % minority SNP | Locus | Gene or product | Effect | Homopolymer |
|---|---|---|---|---|---|---|---|
| 114146 | A (387) | T (27) | 6.52 | HPYLSS1_00109 | hyp. | Nonsynonymous F:L | A |
| 147049 | T (436) | A (41) | 8.60 | HPYLSS1_00135 | fixN | Synonymous | |
| 148431 | A (305) | C (26) | 7.85 | HPYLSS1_00136 | fixO | Synonymous | |
| 186359 | T (221) | C (46) | 17.23 | HPYLSS1_00179 | clsA | Synonymous | |
| 187828 | T (269) | G (48) | 15.14 | HPYLSS1_00181 | frdA | Nonsynonymous K:N | |
| 252785 | A (504) | T (37) | 6.84 | HPYLSS1_00242 | omp | Nonsynonymous Q:H | |
| 252826 | T (1,114) | A (30) | 2.62 | HPYLSS1_00242 | omp | Missense | |
| 253141 | A (430) | T (56) | 11.52 | HPYLSS1_00243 | omp | Nonsynonymous K:I | A |
| 254527 | T (397) | Del (39) | 8.94 | Intergenic | |||
| 329785 | A (683) | T (38) | 5.27 | HPYLSS1_00312 | flgH | Nonsynonymous N:Y | |
| 329895 | A (307) | G (62) | 16.80 | HPYLSS1_00312 | flgH | Synonymous | A |
| 372026 | A (589) | T (45) | 7.10 | HPYLSS1_00353 | hyp. | Nonsynonymous N:Y | |
| 424362 | T (247) | A (41) | 14.24 | HPYLSS1_00411 | Response regulator | Synonymous | |
| 426404 | GTT (265) | CTC (67) | 20.18 | HPYLSS1_00412 | ispDF | Nonsynonymous K:R | T |
| 472864 | T (495) | A (175) | 26.12 | HPYLSS1_00456 | NYN domain | Nonsynonymous K:I | |
| 474596 | A (557) | T (43) | 7.17 | HPYLSS1_00458 | tdhA | Nonsynonymous L:I | |
| 528077 | A (196) | C (29) | 12.89 | HPYLSS1_00513 | hom | Nonsynonymous F:C | |
| 578269 | A (572) | C (27) | 4.51 | HPYLSS1_00562 | tyrS | Nonsynonymous K:Q | A |
| 579815 | T (588) | A (58) | 8.98 | HPYLSS1_00563 | pyrD_2 | Nonsynonymous F:I | |
| 581267 | T (330) | Del (29) | 8.08 | HPYLSS1_00565 | hyp. | Missense | T |
| 582628 | C (4) | A (18) | 81.82 | HPYLSS1_00566 | flhB | Missense | C |
| 675623 | T (948) | A (42) | 4.24 | HPYLSS1_00648 | uvrD | Nonsynonymous N:Y | T |
| 676491 | T (400) | G (35) | 8.05 | HPYLSS1_00649 | taqIM | Nonsynonymous Q:H | |
| 702344 | A (688) | G (35) | 4.84 | Intergenic | |||
| 731566 | T (6) | Del (15) | 28.57 | Intergenic | |||
| 818638 | T (402) | C (69) | 14.65 | HPYLSS1_00957 | ppiD | Synonymous | |
| 818676 | A (430) | G (49) | 10.23 | HPYLSS1_00957 | ppiD | Nonsynonymous F:L | |
| 889231 | T (281) | A (27) | 8.77 | Intergenic | T | ||
| 897376 | T (144) | Del (45) | 23.81 | Intergenic | T | ||
| 918653 | A (213) | C (32) | 13.06 | HPYLSS1_00869 | rnc | Nonsynonymous F:L | |
| 1152909 | T (784) | G (33) | 4.04 | HPYLSS1_01082 | parB | Nonsynonymous N:H | |
| 1153593 | T (785) | A (35) | 4.27 | HPYLSS1_01082 | parB | Nonsynonymous N:Y | T |
| 1153634 | T (755) | A (71) | 8.60 | HPYLSS1_01083 | soj | Nonsynonymous K:I | T |
| 1155502 | A (509) | G (38) | 6.95 | HPYLSS1_01085 | fmt | Synonymous | A |
| 1198398 | T (260) | Del (30) | 10.34 | HPYLSS1_01122 | omp | Missense | T |
| 1205511 | A (628) | G (28) | 4.27 | HPYLSS1_01129 | Na exchanger | Nonsynonymous F:L | A |
| 1237191 | T (222) | A (41) | 15.59 | Intergenic | |||
| 1239091 | A (287) | T (82) | 22.22 | Intergenic | |||
| 1293001 | T (269) | A (29) | 9.73 | HPYLSS1_01216 | nuoH | Synonymous | |
| 1329559 | T (672) | Del (34) | 4.8 | HPYLSS1_01263 | rplV | Missense | T |
| 1329936 | T (570) | G (46) | 7.47 | HPYLSS1_01264 | rpsS | Nonsynonymous Q:H | |
| 1331340 | T (1,505) | C (35) | 2.27 | Intergenic | |||
| 1331598 | T (838) | A (43) | 4.88 | HPYLSS1_01267 | rplD | Missense | |
| 1431054 | A (175) | Del (37) | 17.45 | Intergenic | A | ||
| 1437973 | A (418) | G (62) | 12.92 | Intergenic | |||
| 1438641 | T (1,214) | Del (139) | 10.27 | Intergenic | T | ||
| 1438946 | A (559) | G (38) | 6.37 | HPYLSS1_01366 | hyp. | Nonsynonymous F:S | |
| 1440337 | T (240) | A (60) | 20.00 | HPYLSS1_01368 | DHH family | Synonymous | |
| 1510384 | T (531) | C (27) | 4.84 | HPYLSS1_01436 | plsY | Synonymous | |
| 1511744 | T (1,091) | A (37) | 3.28 | HPYLSS1_01439 | omp | Nonsynonymous L:I | |
| 1512023 | A (1,235) | T (45) | 3.52 | HPYLSS1_01439 | omp | Nonsynonymous N:Y | |
| 1512054 | A (1,012) | Del (35) | 3.3 | HPYLSS1_01439 | omp | Missense | A |
| 1566497 | T (190) | C (23) | 10.80 | HPYLSS1_01480 | MTase | Synonymous | |
| 1589945 | T (282) | Del (26) | 8.4 | Intergenic | T | ||
| 1590568 | A (340) | T (37) | 9.81 | HPYLSS1_01500 | penA | Nonsynonymous L:I | |
| 1607348 | T (943) | A (90) | 8.71 | HPYLSS1_01519 | ribE | Synonymous | |
| 1609179 | T (1,207) | C (34) | 2.74 | HPYLSS1_01522 | metI | Synonymous | |
| 1609811 | T (253) | A (39) | 13.36 | HPYLSS1_01523 | hyp. | Synonymous |
a
Base 1 and Base 2 indicate the two distinct bases, with the number of deduplicated SOLiD sequencing reads supporting each call indicated in parentheses. The data in the “Homopolymer” column indicate whether the site is part of a homopolymer tract of length 3 or greater. The data in the “Gene or product” column indicate whether the SNP is intergenic or within a gene and the putative identity or function of the gene. hyp., hypothetical; omp, putative outer membrane protein.