mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 197 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 99,015 | 0 | T | C | 38.7% | 182.1 / 283.9 | 231 | F205L (TTT→CTT) | ftsW | peptidoglycan glycosyltransferase FtsW |
| * | NC_000913 | 2,109,937 | 0 | A | G | 37.7% | 133.2 / 158.9 | 138 | Y68H (TAC→CAC) | rfbC | dTDP‑4‑dehydrorhamnose 3,5‑epimerase |
| * | NC_000913 | 357,890 | 0 | C | A | 35.9% | 31.7 / 14.0 | 39 | L267F (TTG→TTT) | cynR | DNA‑binding transcriptional dual regulator CynR |
| * | NC_000913 | 332,417 | 0 | C | T | 34.1% | 222.1 / 176.7 | 176 | T16M (ACG→ATG) | pdeL | DNA‑binding transcriptional regulator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 4,296,268 | 0 | T | C | 32.6% | 113.1 / 81.6 | 89 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,326,450 | 0 | T | G | 32.2% | 373.1 / 32.0 | 174 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,535,884 | 0 | G | A | 32.1% | 406.2 / 288.2 | 293 | P234L (CCG→CTG) | ompR | DNA‑binding transcriptional dual regulator OmpR |
| * | NC_000913 | 3,781,150 | 0 | T | G | 32.0% | 175.3 / 18.4 | 100 | intergenic (+133/‑65) | lldD/trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 29.5% | 345.8 / 23.6 | 150 | L41V (TTG→GTG) | cycA | D‑serine/alanine/glycine/:H(+)symporter |
| * | NC_000913 | 3,003,921 | 0 | T | G | 29.4% | 380.1 / 20.8 | 161 | Y145D (TAT→GAT) | xdhC | putative xanthine dehydrogenase iron‑sulfur‑binding subunit XdhC |
| * | NC_000913 | 2,785,327 | 0 | T | G | 29.2% | 244.0 / 18.2 | 107 | intergenic (‑316/+435) | ypjC/ileY | DUF5507 domain‑containing protein YpjC/tRNA‑Ile |
| * | NC_000913 | 2,772,365 | 0 | G | A | 29.2% | 337.0 / 168.9 | 196 | intergenic (‑211/‑953) | yfjU/yfjW | putative arsenate reductase‑like protein YfjU/uncharacterized protein YfjW |
| * | NC_000913 | 4,571,183 | 0 | A | C | 29.0% | 327.8 / 26.9 | 205 | V131G (GTG→GGG) | yjiR | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| * | NC_000913 | 2,833,533 | 0 | T | G | 28.3% | 486.8 / 21.7 | 216 | V353G (GTG→GGG) | norV | anaerobic nitric oxide reductase flavorubredoxin |
| * | NC_000913 | 1,383,722 | 0 | G | A | 27.9% | 275.2 / 44.8 | 136 | F80F (TTC→TTT) | ycjW | DNA‑binding transcriptional repressor YcjW |
| * | NC_000913 | 1,292,458 | 0 | T | A | 27.9% | 252.4 / 35.4 | 111 | intergenic (+93/+51) | galU/hns | UTP‑‑glucose‑1‑phosphate uridylyltransferase/DNA‑binding transcriptional dual regulator H‑NS |
| * | NC_000913 | 1,159,837 | 0 | A | G | 27.8% | 335.4 / 35.5 | 151 | I572T (ATC→ACC) | fhuE | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 27.7% | 109.9 / 27.2 | 65 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,745,397 | 0 | A | C | 27.6% | 201.7 / 17.3 | 146 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 1,292,455 | 0 | C | A | 27.3% | 233.4 / 34.8 | 110 | intergenic (+90/+54) | galU/hns | UTP‑‑glucose‑1‑phosphate uridylyltransferase/DNA‑binding transcriptional dual regulator H‑NS |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 43 (0.200) | 42/448 | 4.5 | 26.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4536973 = | 119 (0.570) | coding (622/981 nt) | nanS | N‑acetyl‑9‑O‑acetylneuraminate esterase | |||||
| * | ? | NC_000913 | = 609350 | NA (NA) | 44 (0.210) | 41/442 | 4.5 | 20.8% | noncoding (1344/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 839230 = | 168 (0.810) | intergenic (‑23/+19) | ybiX/fiu | PKHD‑type hydroxylase YbiX/iron catecholate outer membrane transporter Fiu | |||||
| * | ? | NC_000913 | 608008 = | NA (NA) | 33 (0.160) | 31/442 | 5.6 | 16.7% | noncoding (2/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 839235 | 165 (0.790) | intergenic (‑28/+14) | ybiX/fiu | PKHD‑type hydroxylase YbiX/iron catecholate outer membrane transporter Fiu | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 22 (0.100) | 22/448 | 7.0 | 15.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4536976 | 120 (0.570) | coding (619/981 nt) | nanS | N‑acetyl‑9‑O‑acetylneuraminate esterase | |||||
| * | ? | NC_000913 | = 2067353 | NA (NA) | 9 (0.040) | 9/448 | 10.0 | 7.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4536973 = | 119 (0.570) | coding (622/981 nt) | nanS | N‑acetyl‑9‑O‑acetylneuraminate esterase | |||||
| * | ? | NC_000913 | = 3868543 | 273 (1.300) | 4 (0.020) | 4/446 | 12.0 | 1.5% | coding (767/1248 nt) | yidR | DUF3748 domain‑containing galacturonate catabolism protein YidR |
| ? | NC_000913 | 3868547 = | 271 (1.290) | coding (763/1248 nt) | yidR | DUF3748 domain‑containing galacturonate catabolism protein YidR | |||||
| * | ? | NC_000913 | = 1457343 | 298 (1.420) | 3 (0.020) +22 bp |
3/404 | 12.1 | 2.1% | coding (914/1071 nt) | paaE | phenylacetyl‑CoA 1,2‑epoxidase, reductase subunit |
| ? | NC_000913 | = 4124499 | 7 (0.030) | intergenic (‑43/+113) | cytR/priA | DNA‑binding transcriptional repressor CytR/primosomal protein N' | |||||
| * | ? | NC_000913 | = 2440910 | 292 (1.390) | 3 (0.010) | 3/426 | 12.3 | 1.2% | coding (696/1221 nt) | fabB | 3‑oxoacyl‑[acyl carrier protein] synthase 1 |
| ? | NC_000913 | 3518182 = | 231 (1.150) | coding (305/1089 nt) | aroB | 3‑dehydroquinate synthase | |||||
| * | ? | NC_000913 | = 374185 | 587 (2.790) | 3 (0.020) | 3/420 | 12.3 | 0.76% | coding (318/1014 nt) | mhpE | 4‑hydroxy‑2‑oxovalerate aldolase |
| ? | NC_000913 | = 3091646 | 238 (1.210) | coding (513/732 nt) | rsmE | 16S rRNA m(3)U1498 methyltransferase | |||||
| * | ? | NC_000913 | 3392104 = | 208 (0.990) | 3 (0.010) | 3/430 | 12.4 | 1.5% | intergenic (‑76/+354) | tldD/yhdP | metalloprotease subunit TldD/phospholipid transport factor YhdP |
| ? | NC_000913 | = 3754887 | 197 (0.970) | intergenic (‑459/+86) | yiaW/aldB | DUF3302 domain‑containing protein YiaW/aldehyde dehydrogenase B | |||||