mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,522,362 | 0 | C | T | 69.3% | 222.0 / 137.1 | 176 | G578D (GGC→GAC) | yjhG | KpLE2 phage‑like element; D‑xylonate dehydratase |
| * | NC_000913 | 3,620,983 | 0 | A | G | 48.5% | 54.7 / 133.8 | 102 | I598V (ATC→GTC) ‡ | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,620,984 | 0 | T | C | 43.4% | 97.4 / 122.7 | 113 | I598T (ATC→ACC) ‡ | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,621,001 | 0 | G | A | 39.5% | 194.2 / 170.3 | 173 | A604T (GCC→ACC) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 4,296,060 | 0 | C | T | 33.9% | 142.8 / 96.5 | 109 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.5% | 153.7 / 12.7 | 81 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 32.0% | 246.5 / 48.4 | 157 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.2% | 136.6 / 15.7 | 73 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,111,747 | 0 | G | T | 25.8% | 168.1 / 17.5 | 66 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.4% | 241.9 / 38.4 | 122 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 646,747 | 0 | T | G | 23.4% | 170.7 / 21.3 | 77 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.5% | 307.6 / 18.0 | 139 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 2,601,519 | 0 | G | A | 21.1% | 273.0 / 54.4 | 130 | A107T (GCC→ACC) | hyfA | hydrogenase 4 component A |
| * | NC_000913 | 3,206,444 | 0 | T | A | 20.0% | 283.8 / 10.6 | 120 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 132 (0.890) | 16 (0.120) | 16/258 | 4.3 | 10.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 154 (1.120) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 143 (0.970) | 8 (0.060) | 8/258 | 6.3 | 5.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 154 (1.120) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 728337 = | 148 (1.000) | 14 (0.100) | 8/274 | 6.6 | 11.8% | coding (396/1674 nt) | kdpA | K(+) transporting P‑type ATPase subunit KdpA |
| ? | NC_000913 | 1456665 = | 63 (0.430) | coding (236/1071 nt) | paaE | phenylacetyl‑CoA 1,2‑epoxidase, reductase subunit | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 8 (0.050) +T |
6/274 | 7.3 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4341795 | 146 (0.990) | 4 (0.030) | 4/240 | 7.7 | 3.3% | intergenic (‑167/‑116) | melR/melA | DNA‑binding transcriptional dual regulator MelR/alpha‑galactosidase |
| ? | NC_000913 | = 4341815 | 110 (0.860) | intergenic (‑187/‑96) | melR/melA | DNA‑binding transcriptional dual regulator MelR/alpha‑galactosidase | |||||
| * | ? | NC_000913 | = 381473 | NA (NA) | 6 (0.040) | 4/254 | 7.9 | NA | noncoding (214/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381839 | NA (NA) | noncoding (580/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 353266 = | 110 (0.750) | 4 (0.030) | 4/252 | 7.9 | 3.8% | coding (561/1887 nt) | prpE | propionyl‑CoA synthetase |
| ? | NC_000913 | 353394 = | 103 (0.760) | coding (689/1887 nt) | prpE | propionyl‑CoA synthetase | |||||
| * | ? | NC_000913 | 3279352 = | 113 (0.770) | 5 (0.040) | 4/258 | 8.0 | 4.1% | coding (439/1281 nt) | kbaZ | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ |
| ? | NC_000913 | 3279460 = | 128 (0.930) | coding (547/1281 nt) | kbaZ | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ | |||||
| * | ? | NC_000913 | = 1816202 | NA (NA) | 3 (0.020) | 3/248 | 8.4 | NA | noncoding (17/34 nt) | other | REP129a |
| ? | NC_000913 | = 1816355 | NA (NA) | noncoding (11/30 nt) | other | REPt129c | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 3 (0.020) | 3/256 | 8.5 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||