mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 444,779 | C→T | 100% | W440* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 518,393 | T→C | 13.7% | intergenic (+107/‑324) | ybbP → / → rhsD | putative ABC transporter permease/Rhs family putative polymorphic toxin |
| RA | 568,007 | G→A | 15.3% | G29D (GGC→GAC) | ybcN → | DLP12 prophage; uncharacterized protein |
| RA | 757,265 | C→A | 19.3% | S96S (TCC→TCA) | sucB → | dihydrolipoyltranssuccinase |
| RA | 2,084,016 | Δ1 bp | 25.0% | coding (344/900 nt) | hisG → | ATP phosphoribosyltransferase |
| RA | 2,084,017 | Δ1 bp | 25.0% | coding (345/900 nt) | hisG → | ATP phosphoribosyltransferase |
| RA | 2,261,988 | C→T | 16.8% | R227R (CGC→CGT) | yeiR → | Zn‑stimulated GTPase involved in zinc homeostasis; mutants are cadmium and EDTA sensitive; Zn(2+) binding protein |
| RA | 2,305,946 | G→T | 77.8% | R95S (CGT→AGT) | ompC ← | outer membrane porin protein C |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 60.0% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,419,720 | T→C | 28.4% | D183G (GAT→GGT) | hisJ ← | histidine/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,353 | A→G | 72.2% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| JC | 2,656,840:1 | (GCGCGCA)2→3 | 81.2% | coding (40/804 nt) | suhB → | inositol monophosphatase |
| RA | 2,705,098 | G→A | 15.4% | W440* (TGG→TGA) | nadB → | quinolinate synthase, L‑aspartate oxidase (B protein) subunit |
| RA | 2,775,283 | C→T | 17.2% | G268D (GGC→GAC) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,819,176 | C→A | 21.0% | intergenic (‑241/‑15) | mltB ← / → srlA | membrane‑bound lytic murein transglycosylase B/glucitol/sorbitol‑specific enzyme IIC component of PTS |
| RA | 2,851,857 | C→T | 9.1% | A469V (GCG→GTG) | mutS → | methyl‑directed mismatch repair protein |
| RA | 3,131,672 | Δ1 bp | 16.7% | coding (210/1860 nt) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 23.6% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,371,135 | G→T | 22.9% | intergenic (‑356/+39) | sspA ← / ← rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 |
| RA | 3,378,362 | A→C | 27.4% | S101R (AGC→CGC) | argR → | l‑arginine‑responsive arginine metabolism regulon transcriptional regulator |
| RA | 3,528,506 | A→C | 68.3% | V241G (GTA→GGA) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,651,823 | T→A | 7.9% | I33N (ATC→AAC) | gadE → | gad regulon transcriptional activator |
| RA | 3,676,832 | G→T | 81.1% | intergenic (‑25/+158) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| JC | 3,676,860:1 | (GGTACCTGCGG)1→2 | 89.8% | intergenic (‑53/+130) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 4,022,395 | C→T | 27.1% | G646D (GGC→GAC) | fadB ← | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,356,671 | T→G | 15.8% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 34 (1.440) | 29/270 | NT | NA | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 1045234 = | 23 (0.980) | 11 (0.470) | 9/270 | NT | 44.0% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | CP009273 | = 1973123 | 5 (0.210) | intergenic (‑669/‑111) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1046001 | 26 (1.100) | 21 (0.890) | 19/270 | NT | 57.5% | intergenic (+15/+418) | insB1/cspH | IS1 transposase B/stress protein, member of the CspA‑family |
| ? | CP009273 | 1973115 = | 5 (0.210) | intergenic (‑661/‑119) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 25 (1.060) | 5 (0.240) | 5/238 | NT | 23.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 11 (0.530) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1219684 = | 18 (0.760) | 2 (0.090) | 3/248 | NT | 10.9% | intergenic (+321/+51) | ycgI/minE | pseudogene/cell division topological specificity factor |
| ? | CP009273 | 1219710 = | 16 (0.740) | intergenic (+347/+25) | ycgI/minE | pseudogene/cell division topological specificity factor | |||||
| * | ? | CP009273 | = 2096424 | NA (NA) | 49 (2.080) | 42/270 | NT | 80.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 2427745 | 12 (0.510) | coding (476/660 nt) | dedA | DedA family inner membrane protein | |||||
| * | ? | CP009273 | 3742803 = | 88 (3.740) | 3 (0.140) | 3/254 | NT | 3.4% | coding (212/861 nt) | sgbU | putative L‑xylulose 5‑phosphate 3‑epimerase |
| ? | CP009273 | 3742825 = | 89 (4.020) | coding (234/861 nt) | sgbU | putative L‑xylulose 5‑phosphate 3‑epimerase | |||||