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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 109,394 | G→T | L372L (CTG→CTT) | secA → | protein translocation ATPase |
| RA | 169,074 | G→T | E531* (GAA→TAA) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| JC JC | 310,050 | IS150 (+) +3 bp | intergenic (‑24/+32) | ecpB ← / ← ecpA | putative fimbrial chaperone EcpB/common pilus major subunit |
| MC JC | 364,237 | Δ1,164 bp | coding (906‑2069/3075 nt) | lacZ ← | beta‑galactosidase |
| MC JC | 676,814 | Δ11,037 bp | IS5‑mediated | [ybeR]–gltI | [ybeR], djlB, ybeT, ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 696,450 | G→T | noncoding (55/75 nt) | glnX ← | tRNA‑Gln |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 789,705 | Δ1 bp | coding (275/1149 nt) | galK ← | galactokinase |
| RA | 1,152,846 | C→T | A303V (GCG→GTG) | fabF → | 3‑oxoacyl‑[acyl carrier protein] synthase 2 |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| JC JC | 1,291,049 | IS1 (+) +9 bp | coding (808‑816/1014 nt) | rssB → | regulator of RpoS |
| JC | 1,302,405 | Δ4 bp | coding (1224‑1227/1632 nt) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| JC JC | 1,313,936 | IS2 (+) +5 bp | intergenic (‑273/‑80) | yciC ← / → ompW | putative inner membrane protein/outer membrane protein W |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,358,901 | G→T | P96Q (CCG→CAG) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,367,726 | G→T | L63I (CTT→ATT) | pspF ← | DNA‑binding transcriptional dual regulator PspF |
| MC JC | 1,397,239 | Δ17,203 bp | IS5‑mediated | ynaJ–[recT] | 23 genes ynaJ, uspE, fnr, ogt, abgT, abgB, abgA, abgR, mcaS, smrA, dgcM, ynaN, zntB, fnrS, ynaL, dbpA, ttcA, intR, xisR, rcbA, ralA, ralR, [recT] |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,173,448 | C→T | intergenic (‑575/+834) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,322,099 | C→T | P78P (CCC→CCT) | atoC → | DNA‑binding transcriptional activator/ornithine decarboxylase inhibitor AtoC |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,823,537 | A→G | L78P (CTG→CCG) | recA ← | DNA recombination/repair protein RecA |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,240,844 | G→A | A301T (GCG→ACG) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,441,065 | Δ1 bp | coding (611/621 nt) | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,474,424 | T→G | K43N (AAA→AAC) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,486,415 | C→T | S99L (TCG→TTG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| JC JC | 3,729,449 | IS1 (+) +9 bp | noncoding (89‑97/160 nt) coding (1309‑1317/1323 nt) |
xylZ ← xylA ← |
small RNA XylZ xylose isomerase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| JC JC | 3,933,292 | IS1 (+) +9 bp | intergenic (+108/‑51) | kup → / → rbsD | K(+):H(+) symporter Kup/D‑ribose pyranase |
| RA | 3,938,441 | Δ1 bp | coding (215/993 nt) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| RA | 3,985,729 | C→T | L93L (CTG→CTA) | aslA ← | putative sulfatase AslA |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| JC JC | 4,344,081 | IS2 (–) +5 bp | coding (713‑717/1422 nt) | melB → | melibiose:H(+)/Na(+)/Li(+) symporter |
| JC JC | 4,349,111 | IS2 (+) +5 bp | intergenic (‑367/+200) | dcuB ← / ← dcuR | anaerobic C4‑dicarboxylate transporter DcuB/DNA‑binding transcriptional activator DcuR |
| RA | 4,467,674 | T→G | L17R (CTG→CGG) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| JC JC | 4,598,922 | IS150 (+) +3 bp | coding (518‑520/2292 nt) | opgB ← | phosphoglycerol transferase I |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| JC JC | 4,640,418 | IS30 (–) +2 bp | coding (17‑18/141 nt) | yjjY → | uncharacterized protein YjjY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2996326 | 2997464–2996360 | 35–1139 | 3 [2] | [2] 3 | insD4–[insC4] | insD4,[insC4] |
| * | * | ÷ | NC_000913 | 3423899–3424233 | 3424428–3424238 | 6–530 | 3 [2] | [2] 3 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4035396–4035732 | 4036858–4035736 | 5–1463 | 3 [2] | [2] 3 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 45 (1.010) | 10 (0.230) | 9/480 | 1.9 | 20.9% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 31 (0.700) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 1207790 = | 9 (0.200) | 12 (0.290) | 12/452 | 1.5 | 62.5% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 6 (0.140) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 8 (0.180) | 16 (0.380) | 16/452 | 1.1 | 70.4% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 6 (0.140) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 22 (0.500) | 22/476 | 0.8 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2996343 | NA (NA) | 28 (0.630) | 27/482 | 0.6 | NA | intergenic (+2487/+29) | ygeI/insD4 | protein YgeI/IS2 insertion element protein InsB |
| ? | NC_000913 | 2996361 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||