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 | 17,037 | G→A | 5.6% | intergenic (+31/‑452) | sokC → / → nhaA | antisense RNA blocking mokC and hokC translation/Na(+):H(+) antiporter NhaA |
| RA | 123,466 | T→G | 44.5% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 123,484 | T→G | 16.1% | G156G (GGT→GGG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 198,605 | G→A | 6.9% | L226L (CTG→CTA) | bamA → | outer membrane protein assembly factor BamA |
| RA | 231,512 | T→C | 5.4% | L131L (TTG→CTG) | yafD → | endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| RA | 238,523 | G→T | 27.8% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 39.0% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 279,011 | C→T | 8.6% | pseudogene (152/349 nt) | afuB ← | CP4‑6 prophage; ABC transporter membrane protein AfuB |
| RA | 281,077 | C→T | 5.1% | A303T (GCG→ACG) | yagA ← | CP4‑6 prophage; integrase core domain‑containing protein YagA |
| RA | 307,549 | C→A | 5.6% | G595V (GGT→GTT) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 355,556 | C→A | 8.3% | A212D (GCT→GAT) | codB → | cytosine transporter |
| RA | 377,789 | C→T | 6.7% | A194T (GCC→ACC) | frmB ← | S‑formylglutathione hydrolase FrmB |
| RA | 548,153 | T→G | 25.6% | L492V (TTA→GTA) | fdrA → | putative acyl‑CoA synthetase FdrA |
| RA | 729,372 | A→C | 41.2% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 729,383 | T→G | 37.6% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 746,666 | C→T | 7.4% | I244I (ATC→ATT) | nei → | endonuclease VIII |
| RA | 780,933 | G→C | 22.1% | intergenic (+15/‑135) | lysW → / → valZ | tRNA‑Lys/tRNA‑Val |
| RA | 833,155 | C→T | 7.0% | A29V (GCG→GTG) | dinG → | ATP‑dependent DNA helicase DinG |
| RA | 836,541 | A→G | 5.8% | H64R (CAC→CGC) | hcxB → | hydroxycarboxylate dehydrogenase B |
| RA | 1,166,095 | C→T | 5.6% | P4L (CCA→CTA) | ndh → | NADH:quinone oxidoreductase II |
| RA | 1,253,997 | T→G | 14.8% | K652N (AAA→AAC) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,365,310 | T→C | 7.5% | M360T (ATG→ACG) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,380,827 | C→T | 7.0% | pseudogene (7/969 nt) | ycjV → | putative ABC transporter ATP‑binding protein YcjV |
| RA | 1,425,558 | T→G | 22.9% | V61G (GTT→GGT) | ynaK → | Rac prophage; ParB‑like nuclease domain‑containing protein YnaK |
| RA | 1,478,836 | A→G | 5.5% | K204R (AAA→AGA) | ynbB → | putative CDP‑diglyceride synthase |
| RA | 1,488,358 | G→A | 5.4% | A43T (GCC→ACC) | aldA → | aldehyde dehydrogenase A |
| RA | 1,581,152 | Δ1 bp | 5.8% | coding (1373/1683 nt) | ydeN ← | putative sulfatase |
| RA | 1,581,458 | A→G | 5.9% | L356P (CTG→CCG) | ydeN ← | putative sulfatase |
| RA | 1,727,775 | G→C | 6.0% | intergenic (+19/‑62) | nemA → / → gloA | N‑ethylmaleimide reductase/glyoxalase I |
| RA | 1,923,228 | G→A | 10.3% | noncoding (163/249 nt) | ryeA → | small RNA RyeA |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,064,628 | Δ1 bp | 8.3% | coding (595/744 nt) | cobS ← | cobalamin 5'‑phosphate synthase |
| RA | 2,139,598 | T→G | 31.9% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,302,247 | C→T | 6.4% | S169S (TCG→TCA) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,303,932 | T→A | 8.7% | F10I (TTT→ATT) | eco → | serine protease inhibitor ecotin |
| RA | 2,362,624 | A→C | 5.1% | F337C (TTT→TGT) | yfaY ← | IPR008135 CinA family protein YfaY |
| RA | 2,470,436 | C→A | 45.9% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,604,704 | A→G | 8.9% | A286A (GCA→GCG) | hyfC → | hydrogenase 4 component C |
| RA | 2,717,320 | G→A | 6.2% | S189S (TCG→TCA) | ung → | uracil‑DNA glycosylase |
| RA | 2,925,879 | G→T | 6.3% | E178* (GAA→TAA) | queF → | 7‑cyano‑7‑deazaguanine reductase |
| RA | 2,980,920 | G→A | 5.0% | S421S (AGC→AGT) | araE ← | arabinose:H(+) symporter |
| RA | 3,044,828 | T→G | 9.2% | D389E (GAT→GAG) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,114,231 | T→C | 5.3% | Q41R (CAA→CGA) | pppA ← | prepilin peptidase |
| RA | 3,137,650 | G→A | 6.1% | F291F (TTC→TTT) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,140,231 | A→C | 18.5% | W30G (TGG→GGG) | hybF ← | hydrogenase maturation protein HybF |
| RA | 3,316,313 | G→A | 10.3% | A405V (GCA→GTA) | nusA ← | transcription termination/antitermination protein NusA |
| RA | 3,328,312 | T→C | 6.0% | E135G (GAA→GGA) | greA ← | transcription elongation factor GreA |
| RA | 3,454,069 | G→T | 47.5% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,589,910 | C→T | 6.3% | A40T (GCC→ACC) | ugpE ← | sn‑glycerol 3‑phosphate ABC transporter membrane subunit UgpE |
| RA | 3,815,828 | T→G | 41.9% | intergenic (‑60/+35) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| RA | 3,977,979 | C→T | 8.2% | T152M (ACG→ATG) | rffT → | 4‑acetamido‑4,6‑dideoxy‑D‑galactose transferase |
| MC JC | 4,123,449 | Δ990 bp | 100% | coding (19‑1008/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,125,509 | C→T | 5.6% | L434L (CTG→CTA) | priA ← | primosome factor N' |
| RA | 4,183,258 | G→A | 70.3% | E672K (GAA→AAA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,199,178 | T→G | 24.5% | V130G (GTG→GGG) | nfi → | endonuclease V |
| RA | 4,296,060 | C→T | 27.3% | 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 | 4,347,505 | G→A | 7.2% | R414C (CGC→TGC) | dcuB ← | anaerobic C4‑dicarboxylate transporter DcuB |
| RA | 4,469,283 | G→T | 6.5% | P553P (CCG→CCT) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,568,692 | T→A | 8.2% | intergenic (‑173/‑306) | mdtM ← / → rpnD | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter/truncated recombination‑promoting nuclease‑like protein RpnD |
| RA | 4,606,205 | C→G | 45.2% | noncoding (82/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,629,075 | A→C | 17.8% | L483R (CTG→CGG) | ettA ← | energy‑dependent translational throttle protein EttA |
| RA | 4,631,660 | C→T | 8.0% | Q310* (CAA→TAA) | slt → | soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423753–3424234 | 3424544–3424239 | 6–792 | 17 [16] | [16] 17 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 291401 | NA (NA) | 6 (0.100) | 6/234 | NT | 12.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3842904 | 43 (0.750) | coding (886/1335 nt) | adeQ | adenine transporter | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 5 (0.090) | 5/234 | NT | 7.4% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1292989 = | 63 (1.100) | intergenic (‑67/‑538) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 33 (0.580) | 39 (0.790) | 26/202 | NT | 59.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 24 (0.490) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.510) | 27 (0.550) | 22/202 | NT | 52.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 24 (0.490) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 67 (1.210) | 44/226 | 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 | 1978503 = | NA (NA) | 15 (0.260) | 14/234 | NT | 14.7% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3710132 = | 87 (1.520) | coding (344/1692 nt) | eptB | Kdo2‑lipid A phosphoethanolamine 7''‑transferase | |||||