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 119 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,715,336 | 0 | G | T | 69.3% | 95.6 / 69.5 | 75 | P353P (CCC→CCA) | bisC | biotin sulfoxide reductase |
| * | NC_000913 | 912,973 | 0 | G | T | 64.1% | 71.1 / 83.4 | 78 | P281Q (CCG→CAG) | hcp | protein S‑nitrosylase |
| * | NC_000913 | 339,986 | 0 | G | A | 62.8% | 40.2 / 40.1 | 43 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 2,392,378 | 0 | G | T | 60.7% | 42.9 / 108.9 | 89 | L222M (CTG→ATG) | nuoM | NADH:quinone oxidoreductase subunit M |
| * | NC_000913 | 339,979 | 0 | G | A | 60.5% | 35.4 / 43.1 | 43 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 4,430,053 | 0 | G | T | 59.7% | 66.6 / 154.0 | 125 | G64C (GGT→TGT) | cycA | D‑serine/alanine/glycine/:H(+)symporter |
| * | NC_000913 | 3,683,243 | 0 | C | T | 59.2% | 90.2 / 156.6 | 121 | A69T (GCG→ACG) | dctA | C4 dicarboxylate/orotate:H(+) symporter |
| * | NC_000913 | 1,565,245 | 0 | G | T | 58.7% | 43.6 / 148.6 | 109 | R163R (CGC→CGA) | dosP | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| * | NC_000913 | 2,136,464 | 0 | C | A | 56.9% | 18.0 / 144.5 | 102 | M260I (ATG→ATT) | wza | outer membrane polysaccharide export protein Wza |
| * | NC_000913 | 2,358,126 | 0 | C | A | 56.8% | 21.1 / 131.0 | 95 | T240T (ACG→ACT) | yfaU | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| * | NC_000913 | 1,102,600 | 0 | G | T | 56.4% | 58.1 / 170.2 | 133 | A199A (GCC→GCA) | csgD | DNA‑binding transcriptional dual regulator CsgD |
| * | NC_000913 | 2,410,025 | 0 | G | T | 56.0% | 7.4 / 119.8 | 84 | A443D (GCT→GAT) | yfbS | putative transporter YfbS |
| * | NC_000913 | 1,004,355 | 0 | C | A | 55.9% | 14.3 / 135.6 | 93 | R137S (CGC→AGC) | ycbF | putative fimbrial chaperone YcbF |
| * | NC_000913 | 1,560,067 | 0 | C | A | 55.6% | 18.7 / 168.1 | 117 | G288V (GGA→GTA) | ddpB | putative D,D‑dipeptide ABC transporter membrane subunit DdpB |
| * | NC_000913 | 4,428,199 | 0 | C | A | 55.3% | 17.0 / 168.7 | 114 | Q173H (CAG→CAT) | ytfB | cell division protein YtfB |
| * | NC_000913 | 556,379 | 0 | C | A | 55.1% | 7.9 / 157.0 | 107 | G59W (GGG→TGG) | ybcI | PF04307 family inner membrane protein YbcI |
| * | NC_000913 | 2,566,104 | 0 | G | T | 55.1% | ‑2.3 / 104.9 | 69 | L261I (CTT→ATT) | eutA | ethanolamine ammonia‑lyase reactivase EutA |
| * | NC_000913 | 2,771,886 | 0 | A | C | 54.8% | 61.9 / 217.0 | 156 | F90C (TTT→TGT) | yfjU | putative arsenate reductase‑like protein YfjU |
| * | NC_000913 | 2,136,327 | 0 | C | A | 54.7% | 9.3 / 137.1 | 95 | G306V (GGC→GTC) | wza | outer membrane polysaccharide export protein Wza |
| * | NC_000913 | 2,564,513 | 0 | G | T | 54.7% | 28.1 / 191.0 | 139 | intergenic (+141/‑10) | yffR/yffS | uncharacterized protein YffR/uncharacterized protein YffS |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 161 (1.520) | 29 (0.280) | 26/580 | 3.1 | 16.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 131 (1.270) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4316493 | 40 (0.380) | 35 (0.340) | 25/588 | 3.3 | 47.5% | coding (726/1137 nt) | phnM | RPnTP hydrolase |
| ? | NC_000913 | 4316545 = | 38 (0.360) | coding (674/1137 nt) | phnM | RPnTP hydrolase | |||||
| * | ? | NC_000913 | 4542682 = | 160 (1.510) | 29 (0.280) | 22/580 | 3.8 | 16.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 132 (1.280) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1411899 = | 130 (1.220) | 16 (0.170) | 14/546 | 5.3 | 10.8% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 146 (1.510) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 2653419 | 90 (0.850) | 12 (0.120) | 10/548 | 6.6 | 12.5% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 85 (0.870) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2947467 | 105 (0.990) | 5 (0.070) | 5/432 | 7.4 | 6.7% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 63 (0.820) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 1286906 | 54 (0.510) | 10 (0.100) | 7/558 | 7.9 | 15.7% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 57 (0.580) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2817942 | 80 (0.750) | 5 (0.050) | 5/558 | 8.9 | 6.1% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 79 (0.800) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 2153357 | 125 (1.180) | 5 (0.050) | 4/576 | 9.7 | 4.4% | noncoding (47/144 nt) coding (52/60 nt) |
sibA ibsA |
small RNA SibA toxic peptide IbsA |
| ? | NC_000913 | 2153690 = | 99 (0.970) | noncoding (45/136 nt) coding (48/57 nt) |
sibB ibsB |
small RNA SibB putative toxic peptide IbsB |
|||||
| * | ? | NC_000913 | = 781016 | 47 (0.440) | 4 (0.040) | 3/524 | 9.8 | 5.9% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
| ? | NC_000913 | 781809 = | 86 (0.920) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||