mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 68,486 | T→G | 14.1% | L217V (TTG→GTG) | yabI → | DedA family inner membrane protein |
| RA | 161,068 | A→C | 18.3% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 187,722 | G→T | 6.1% | G127C (GGT→TGT) | tsf → | translation elongation factor EF‑Ts |
| RA | 221,373:1 | +G | 7.3% | noncoding (1116/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,380 | T→A | 7.3% | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,390 | Δ1 bp | 7.5% | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,391 | G→A | 7.5% | noncoding (1134/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,393 | C→T | 7.6% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,395 | G→A | 7.5% | noncoding (1138/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,397 | C→T | 7.6% | noncoding (1140/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,398 | C→T | 7.5% | noncoding (1141/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,402 | A→C | 7.7% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 7.9% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 8.5% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 8.7% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 12.1% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 12.9% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 17.1% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 14.4% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,471 | C→T | 14.9% | noncoding (1214/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,476 | A→T | 17.8% | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 249,874 | G→C | 5.2% | intergenic (+226/‑92) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 286,409 | T→A | 8.1% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 295,695 | T→G | 5.0% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 418,995 | T→G | 10.3% | L341R (CTG→CGG) | malZ → | maltodextrin glucosidase |
| RA | 577,301 | T→C | 5.6% | pseudogene (186/438 nt) | tfaD → | pseudogene, DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related |
| RA | 694,871 | A→C | 5.5% | intergenic (‑238/+159) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 780,417 | G→T | 17.1% | T119T (ACC→ACA) | ybgS ← | putative periplasmic protein |
| RA | 910,671 | T→G | 11.6% | intergenic (‑358/+137) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 910,682 | T→G | 10.2% | intergenic (‑369/+126) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 910,683 | G→C | 8.6% | intergenic (‑370/+125) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 950,067 | C→A | 7.2% | intergenic (‑145/+261) | focA ← / ← ycaO | formate channel/ribosomal protein S12 methylthiotransferase accessory factor |
| RA | 1,282,493 | C→G | 6.6% | intergenic (+511/+29) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,321,059 | G→T | 9.0% | intergenic (+161/‑50) | yciQ → / → rluB | enhancer of membrane protein expression; putative inner membrane protein/23S rRNA pseudouridine(2605) synthase |
| RA | 1,336,205 | C→A | 5.2% | R10S (CGC→AGC) | pyrF → | orotidine‑5'‑phosphate decarboxylase |
| RA | 1,460,602 | T→C | 5.4% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,819 | G→A | 6.1% | pseudogene (1171/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,861 | G→A | 9.6% | pseudogene (1213/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,896 | C→T | 9.7% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,461,046 | C→T | 5.6% | pseudogene (1398/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,628,897 | G→C | 6.6% | G82G (GGC→GGG) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,628,900 | G→T | 6.6% | S81S (TCC→TCA) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,628,903 | A→C | 6.4% | A80A (GCT→GCG) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,628,906 | C→T | 6.7% | V79V (GTG→GTA) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,828,729 | A→C | 11.4% | E119D (GAA→GAC) | ydjY → | putative ferrodoxin‑like lipoprotein |
| RA | 2,019,261 | Δ1 bp | 5.5% | coding (270/816 nt) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,019,262 | Δ1 bp | 5.5% | coding (271/816 nt) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,019,263 | Δ1 bp | 5.5% | coding (272/816 nt) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,019,264 | Δ1 bp | 5.5% | coding (273/816 nt) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,022,779 | G→T | 5.6% | S23S (TCC→TCA) | yedI ← | DUF808 family inner membrane protein |
| RA | 2,075,847 | G→T | 5.6% | P61H (CCC→CAC) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6b) |
| RA | 2,168,864 | C→T | 5.9% | A313T (GCG→ACG) | gatZ ← | D‑tagatose 1,6‑bisphosphate aldolase 2, subunit |
| RA | 2,186,584 | C→A | 5.4% | W355L (TGG→TTG) | mrp ← | antiporter inner membrane protein |
| RA | 2,222,656 | A→C | 9.3% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,310,490 | A→G | 6.7% | intergenic (+184/+16) | rcsB → / ← rcsC | response regulator in two‑component regulatory system with RcsC and YojN/hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,312,673 | G→T | 5.8% | T228N (ACC→AAC) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,356,740 | C→T | 5.2% | A125T (GCT→ACT) | yfaY ← | inactive PncC family protein |
| RA | 2,464,580 | A→C | 5.2% | pseudogene (287/291 nt) T139T (ACT→ACG) |
tfaS → yfdK ← |
pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related CPS‑53 (KpLE1) prophage; conserved protein |
| RA | 2,471,432 | C→A | 7.3% | A36D (GCC→GAC) | dsdX → | D‑serine transporter |
| RA | 2,719,426 | T→C | 88.1% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,748,729 | C→A | 5.5% | H159N (CAC→AAC) | smpB → | trans‑translation protein |
| RA | 2,811,408 | T→A | 7.2% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 3,064,718 | T→G | 9.9% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,187,054 | C→A | 5.2% | R278S (CGT→AGT) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,384,766 | A→C | 5.8% | F208V (TTT→GTT) | tldD ← | putative peptidase |
| RA | 3,416,890 | T→G | 7.3% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 11.4% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,525,250 | C→A | 5.8% | W183C (TGG→TGT) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,562,555 | A→C | 7.4% | V45G (GTA→GGA) | glgC ← | glucose‑1‑phosphate adenylyltransferase |
| RA | 3,602,066 | G→T | 9.4% | intergenic (+57/+45) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,877,923 | A→G | 100% | Q24R (CAG→CGG) | rnpA → | protein C5 component of RNase P |
| RA | 3,952,817 | T→G | 7.6% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,991,439 | A→C | 7.0% | S33R (AGT→CGT) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 3,997,369 | C→A | 10.5% | C57F (TGC→TTC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,019,993 | Δ1 bp | 100% | coding (107/702 nt) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,149,055 | C→A | 8.1% | A213E (GCG→GAG) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,161,576 | A→C | 5.4% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,165,449 | C→T | 8.0% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 8.3% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,177,586 | T→C | 100% | L770P (CTC→CCC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,202,979 | A→C | 19.3% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,286,118 | A→G | 6.3% | intergenic (+396/+135) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,286,119 | A→C | 8.5% | intergenic (+397/+134) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,498,944 | G→A | 5.2% | pseudogene (119/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,532,875 | G→T | 5.8% | intergenic (+425/‑57) | fimE → / → fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| RA | 4,586,629 | C→A | 7.1% | H275N (CAT→AAT) | yjjN → | L‑galactonate oxidoreductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 463842 | 464276 | 435 | 30 [4] | [2] 16 | ybaO | putative DNA‑binding transcriptional regulator |
| * | * | ÷ | CP009273 | 578962 | 579056 | 95 | 7 [3] | [5] 7 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 233 (1.110) | 314 (1.490) | 70/250 | NT | 57.4% | 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 | = 1046001 | 356 (1.690) | 91 (0.430) | 41/250 | NT | 33.0% | intergenic (+15/+418) | insB1/cspH | IS1 transposase B/stress protein, member of the CspA‑family |
| ? | CP009273 | = 1972777 | 13 (0.060) | intergenic (‑323/‑457) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 79 (0.380) | 64 (0.350) | 32/218 | NT | 57.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 26 (0.140) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 81 (0.390) | 91 (0.500) | 36/218 | NT | 65.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 26 (0.140) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972769 = | 17 (0.080) | 112 (0.540) | 47/248 | NT | 86.9% | intergenic (‑315/‑465) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||