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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 51,870 | C→G | 10.2% | V187V (GTG→GTC) | rsmA ← | 16S rRNA m(6)2A1518,m(6)2A1519 dimethyltransferase |
| RA | 88,161 | A→G | 10.2% | H45R (CAC→CGC) | cra → | DNA‑binding transcriptional dual regulator Cra |
| RA | 238,497 | G→T | 21.6% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 307,186 | G→T | 12.5% | S716* (TCA→TAA) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 492,044 | A→G | 13.3% | intergenic (+81/‑48) | apt → / → dnaX | adenine phosphoribosyltransferase/DNA polymerase III subunit tau |
| RA | 626,998 | C→T | 11.1% | A310V (GCA→GTA) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| RA | 744,378 | Δ1 bp | 12.9% | coding (136/933 nt) | pxpC → | 5‑oxoprolinase component C |
| MC JC | 932,613 | Δ459 bp | 100% | coding (19‑477/495 nt) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,109,125 | Δ1 bp | 10.5% | intergenic (‑184/‑210) | opgC ← / → opgG | protein required for succinyl modification of osmoregulated periplasmic glucans/osmoregulated periplasmic glucans (OPGs) biosynthesis protein G |
| RA | 1,137,190 | C→T | 9.5% | P306L (CCA→CTA) | flgI → | flagellar P‑ring protein |
| RA | 1,252,563 | G→C | 13.6% | G500R (GGC→CGC) | dhaR → | DNA‑binding transcriptional dual regulator DhaR |
| RA | 1,277,302 | C→T | 12.1% | W106* (TGG→TAG) | narX ← | sensory histidine kinase NarX |
| RA | 1,398,448 | C→T | 10.8% | A59T (GCT→ACT) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,492,979 | Δ1 bp | 10.3% | coding (510/1641 nt) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,492,980 | Δ1 bp | 10.3% | coding (511/1641 nt) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,492,981 | Δ1 bp | 10.3% | coding (512/1641 nt) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,492,982 | Δ1 bp | 10.3% | coding (513/1641 nt) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,701,239 | T→A | 10.0% | S95T (TCT→ACT) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| RA | 1,836,740 | T→C | 13.1% | V223A (GTC→GCC) | ynjB → | putative ABC transporter periplasmic binding protein YnjB |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,083,752 | Δ1 bp | 13.3% | coding (997/1428 nt) | sbcB → | exodeoxyribonuclease I |
| RA | 2,138,040 | C→T | 9.8% | R47W (CGG→TGG) | yegH → | inner membrane protein YegH |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,245 | G→T | 52.8% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,224,148 | A→G | 13.8% | C241C (TGT→TGC) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,490,148 | G→A | 8.3% | I13I (ATC→ATT) | yfdV ← | putative transport protein YfdV |
| RA | 2,829,156 | G→A | 12.5% | R37H (CGC→CAC) | srlR → | DNA‑binding transcriptional repressor SrlR |
| RA | 3,021,851 | C→T | 5.1% | T179I (ACT→ATT) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,115,949 | G→A | 5.6% | P1055L (CCG→CTG) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,117,310 | C→G | 6.4% | K601N (AAG→AAC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,166,424 | T→C | 5.2% | Q432R (CAG→CGG) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,174,383 | A→G | 5.5% | S338S (TCT→TCC) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,188,976 | C→A | 21.5% | pseudogene (1545/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,418,500 | T→A | 31.0% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,447,122 | A→T | 10.2% | I106N (ATT→AAT) | rplE ← | 50S ribosomal subunit protein L5 |
| RA | 3,527,894 | A→T | 9.1% | I476F (ATT→TTT) | igaA → | inner membrane protein ‑ inhibits the Rcs signaling pathway |
| RA | 3,530,853 | A→G | 8.2% | D529D (GAT→GAC) | yhgE ← | putative transport protein YhgE |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,672,390 | T→C | 10.5% | intergenic (‑496/‑24) | yhjB ← / → yhjC | putative DNA‑binding transcriptional regulator YhjB/putative DNA‑binding transcriptional regulator YhjC |
| RA | 3,750,797 | C→G | 30.6% | intergenic (+16/+331) | sgbE → / ← yiaT | L‑ribulose‑5‑phosphate 4‑epimerase SgbE/outer membrane protein YiaT |
| RA | 3,769,311 | A→G | 5.2% | intergenic (+421/‑34) | yibS → / → yibV | RHS family protein YibS/PF15596 family protein YibV |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,828,980 | A→C | 43.3% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 4,045,402 | G→A | 6.9% | A402T (GCA→ACA) | yihF → | uncharacterized protein YihF |
| RA | 4,175,680 | T→A | 9.5% | noncoding (8/75 nt) | glyT → | tRNA‑Gly |
| RA | 4,183,814 | T→A | 70.7% | V857E (GTG→GAG) | rpoB → | RNA polymerase subunit beta |
| JC | 4,188,490 | +CGT | 17.0% | coding (3141/4224 nt) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,193,487 | C→T | 13.8% | Q30Q (CAG→CAA) | thiF ← | ThiS adenylyltransferase |
| RA | 4,236,912 | A→G | 11.4% | I6V (ATT→GTT) | yjbG → | capsule biosynthesis GfcC family protein YjbG |
| RA | 4,296,060 | C→T | 24.3% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,503,087 | Δ1 bp | 14.3% | coding (345/1329 nt) | insG ← | KpLE2 phage‑like element; IS4 putative transposase |
| RA | 4,605,895 | A→T | 12.8% | Q31L (CAG→CTG) | yjjZ → | protein YjjZ |
| RA | 4,608,739 | G→A | 9.7% | V32I (GTC→ATC) | yjjG → | pyrimidine nucleotidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423775–3424234 | 3424541–3424239 | 6–767 | 7 [6] | [6] 7 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 21 (0.600) | 15 (0.500) | 14/200 | NT | 47.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 15 (0.500) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 49 (1.450) | 36/224 | NT | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2990716 = | 59 (1.680) | 55 (1.570) | 43/232 | NT | 48.2% | pseudogene (163/490 nt) | ygeF | protein YgeF |
| ? | NC_000913 | 3130146 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||