mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 52.0% | 39.7 / 113.4 | 75 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 44.4% | 36.4 / 21.4 | 36 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 41.7% | 33.7 / 17.5 | 36 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 770,897 | 0 | T | G | 39.6% | 60.9 / 14.1 | 48 | intergenic (+286/‑561) | mngB/cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| * | NC_000913 | 735,005 | 0 | G | T | 39.6% | 105.7 / 118.6 | 91 | pseudogene (786/1434 nt) | ybfO | conserved protein, rhs‑like YbfO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 37.3% | 66.5 / 43.3 | 59 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 32.0% | 90.8 / 15.2 | 50 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.2% | 60.7 / 18.4 | 32 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 445,558 | 0 | A | C | 31.0% | 47.7 / 15.4 | 29 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,206,444 | 0 | T | A | 30.5% | 101.1 / 19.8 | 59 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.3% | 175.2 / 49.3 | 89 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.7% | 130.0 / 58.5 | 80 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,825,061 | 0 | G | A | 27.7% | 95.0 / 11.3 | 47 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 1,775,467 | 0 | A | C | 27.4% | 130.7 / 12.5 | 62 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 27.3% | 112.9 / 16.6 | 66 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 646,747 | 0 | T | G | 26.8% | 148.8 / 36.9 | 71 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 26.0% | 116.2 / 11.4 | 50 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 3,915,866 | 0 | T | G | 24.6% | 121.5 / 11.1 | 57 | Y36S (TAC→TCC) | atpC | ATP synthase F1 complex subunit epsilon |
| * | NC_000913 | 1,577,123 | 0 | A | C | 23.6% | 270.3 / 22.3 | 110 | V166G (GTA→GGA) | yddB | putative TonB‑dependent receptor |
| * | NC_000913 | 2,782,509 | 0 | A | C | 22.4% | 271.2 / 19.4 | 117 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 74 (0.840) | 15 (0.190) | 14/244 | 3.8 | 19.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 58 (0.740) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 74 (0.840) | 8 (0.100) | 8/258 | 5.9 | 10.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 67 (0.810) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 76 (0.860) | 8 (0.100) | 7/258 | 6.3 | 10.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 67 (0.810) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 340006 | NA (NA) | 4 (0.060) +29 bp |
4/216 | 6.8 | NA | noncoding (18/29 nt) | other | REPv23f |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 339820 | NA (NA) | 3 (0.040) +29 bp |
3/216 | 7.4 | NA | noncoding (18/29 nt) | other | REPv23b |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 3045995 = | 73 (0.830) | 4 (0.050) | 3/264 | 8.4 | 5.6% | intergenic (‑94/+173) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase |
| ? | NC_000913 | 3046081 = | 65 (0.770) | intergenic (‑180/+87) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase | |||||
| * | ? | NC_000913 | = 779609 | 64 (0.730) | 3 (0.040) | 3/262 | 8.4 | 5.2% | coding (12/792 nt) | cpoB | cell division coordinator CpoB |
| ? | NC_000913 | = 779635 | 49 (0.590) | coding (38/792 nt) | cpoB | cell division coordinator CpoB | |||||
| * | ? | NC_000913 | 334963 = | 117 (1.330) | 3 (0.040) | 3/262 | 8.4 | 2.6% | coding (60/498 nt) | yahC | uncharacterized protein YahC |
| ? | NC_000913 | 335766 = | 117 (1.400) | coding (487/606 nt) | yahD | ankyrin repeat‑containing protein YahD | |||||