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 | annotation | gene | description |
| RA | 73,374 | C→A | G383V (GGG→GTG) | thiP ← | thiamine ABC transporter membrane subunit |
| RA | 205,699 | C→A | R192S (CGC→AGC) | dnaE → | DNA polymerase III subunit alpha |
| RA | 225,658 | T→A | intergenic (+83/‑101) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 399,409 | G→T | intergenic (‑76/‑184) | yaiY ← / → yaiZ | inner membrane protein/DUF2754 domain‑containing protein YaiZ |
| RA | 644,511 | C→A | D165Y (GAC→TAC) | rna ← | RNase I |
| RA | 823,340 | C→A | E134* (GAG→TAG) | clsB ← | cardiolipin synthase B |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 940,030 | G→T | Q201H (CAG→CAT) | serS → | serine‑‑tRNA ligase |
| RA | 941,635 | C→A | P226Q (CCG→CAG) | dmsA → | dimethyl sulfoxide reductase subunit A |
| RA | 1,030,922 | G→T | A166E (GCG→GAG) | yccA ← | modulator of FtsH protease |
| RA | 1,105,928 | G→C | A37P (GCC→CCC) | ymdB → | 2'‑O‑acetyl‑ADP‑ribose deacetylase, regulator of RNase III activity |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,277,749 | C→A | intergenic (‑131/‑208) | narX ← / → narK | sensory histidine kinase NarX/nitrate:nitrite antiporter NarK |
| RA | 1,281,028 | G→A | G389S (GGT→AGT) | narG → | nitrate reductase A subunit alpha |
| RA | 1,474,382 | T→G | D54E (GAT→GAG) | pdxI → | pyridoxine 4‑dehydrogenase |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,754,091 | C→A | P129P (CCG→CCT) | ydhY ← | putative 4Fe‑4S ferredoxin‑type protein |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,010,046 | G→T | A76S (GCC→TCC) | yedK → | putative SOS response‑associated peptidase YedK |
| RA | 2,116,466 | G→A | T221M (ACG→ATG) | wcaL ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,116,992 | G→T | H46N (CAC→AAC) | wcaL ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,270,711 | G→T | intergenic (+166/‑15) | mepS → / → pdeN | peptidoglycan DD‑endopeptidase/peptidoglycan LD‑carboxypeptidase/putative c‑di‑GMP phosphodiesterase PdeN |
| RA | 2,618,210 | C→A | V189V (GTG→GTT) | hda ← | inibitor of reinitiation of DNA replication |
| RA | 2,801,775 | C→A | T143K (ACG→AAG) | nrdE → | ribonucleoside‑diphosphate reductase 2 subunit alpha |
| RA | 2,887,187 | C→A | W11C (TGG→TGT) | cas3 ← | CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 2,937,824 | C→A | S119S (TCC→TCA) | fucK → | L‑fuculokinase |
| RA | 3,062,257 | C→A | L470I (CTT→ATT) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,161,110 | G→T | L13M (CTG→ATG) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,287,474 | G→T | A17S (GCA→TCA) | yraH → | putative fimbrial protein YraH |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,392,980 | G→T | P1093P (CCC→CCA) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,537,853 | G→T | A157S (GCC→TCC) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,629,562 | G→C | D347E (GAC→GAG) | yhiI ← | putative membrane fusion protein YhiI |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,861,907 | C→A | Q27H (CAG→CAT) | glvG ← | putative inactive phospho‑glucosidase |
| JC JC | 3,898,164 | IS2 (–) +5 bp | coding (143‑147/588 nt) | cbrC → | UPF0167 family colicin E2 tolerance protein CbrC |
| RA | 3,945,882 | C→A | noncoding (2179/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,972,258 | T→G | N333K (AAT→AAG) | wecC → | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| RA | 4,119,723 | G→T | R209R (CGC→CGA) | menA ← | 1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase |
| RA | 4,180,365 | G→T | D124Y (GAC→TAC) | rplJ → | 50S ribosomal subunit protein L10 |
| RA | 4,220,905 | G→A | P528L (CCA→CTA) | arpA ← | regulator of acetyl CoA synthetase |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,394,408 | G→T | A115S (GCG→TCG) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| JC JC | 4,410,305 | IS1 (+) +9 bp | coding (173‑181/402 nt) | yjfI → | conserved protein YjfI |
| RA | 4,463,596 | G→A | H372Y (CAT→TAT) | treC ← | trehalose‑6‑phosphate hydrolase |
| RA | 4,488,353 | G→A | A346T (GCC→ACC) | lptG → | lipopolysaccharide transport system protein LptG |
| RA | 4,526,281 | G→T | S203* (TCG→TAG) | sgcR ← | KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator SgcR |
| RA | 4,573,795 | G→T | S461I (AGC→ATC) | yjiT → | putative uncharacterized protein YjiT |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196270 | 1211436 | 15167 | 41 [37] | [37] 43 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3102954 | 3104092 | 1139 | 39 [38] | [38] 39 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423750–3424534 | 3424534 | 1–785 | 39 [38] | [36] 39 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 171 (1.400) | 88/270 | 0.0 | 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 | 3363001 = | 167 (1.330) | 200 (1.600) | 93/276 | 0.0 | 70.0% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 6 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 142 (1.130) | 69/278 | 0.2 | 95.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 7 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||