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 | 61,440 | 2 bp→AA | coding (1824‑1825/2907 nt) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 159,169 | T→A | intergenic (‑43/+17) | pcnB ← / ← gluQ | poly(A) polymerase I/glutamyl‑Q tRNA(Asp) synthetase |
| RA | 202,464 | C→A | R122S (CGC→AGC) | fabZ → | 3‑hydroxy‑acyl‑[acyl‑carrier‑protein] dehydratase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 364,753 | 2 bp→CC | coding (1552‑1553/3075 nt) | lacZ ← | beta‑galactosidase |
| RA | 403,038 | C→T | S431L (TCA→TTA) | phoA → | alkaline phosphatase |
| RA | 404,238 | 2 bp→TT | coding (536‑537/1116 nt) | dgcC → | diguanylate cyclase DgcC |
| RA | 456,803 | A→T | I43F (ATT→TTT) | clpP → | ATP‑dependent Clp protease proteolytic subunit |
| JC JC | 485,359 | IS2 (–) +5 bp | coding (257‑261/1194 nt) | acrA ← | multidrug efflux pump membrane fusion lipoprotein AcrA |
| RA | 566,597 | T→C | intergenic (‑619/‑87) | intD ← / → renD | putative integrase/protein RenD |
| JC JC | 577,400 | IS3 (–) +3 bp | coding (3‑5/216 nt) | essD → | putative phage lysis protein |
| RA | 581,322 | C→T | A163A (GCC→GCT) | nohD → | putative DNA‑packaging protein NohD |
| RA | 581,337 | G→A | L168L (CTG→CTA) | nohD → | putative DNA‑packaging protein NohD |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| RA | 617,061 | G→T | G969W (GGG→TGG) | entF → | apo‑serine activating enzyme |
| JC JC | 637,142 | IS3 (–) +3 bp | coding (475‑477/903 nt) | ybdO ← | putative LysR family DNA‑binding transcriptional regulator YbdO |
| MC JC | 674,957 | Δ12,894 bp | IS5‑mediated | ybeL–gltI | ybeL, ybeQ, ybeR, djlB, ybeT, ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| JC JC | 691,512 | IS3 (–) +3 bp | coding (271‑273/879 nt) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 706,759 | G→A | E223K (GAA→AAA) | glnS → | glutamine‑‑tRNA ligase |
| RA | 708,774 | G→A | A147A (GCG→GCA) | chiP → | chitooligosaccharide outer membrane channel |
| RA | 881,614 | C→T | T296T (ACC→ACT) | dacC → | D‑alanyl‑D‑alanine carboxypeptidase DacC |
| RA | 997,536 | T→C | intergenic (‑24/‑332) | ssuE ← / → elfA | NADPH‑dependent FMN reductase/putative laminin‑binding fimbrial subunit |
| RA | 1,023,187 | C→T | G233R (GGA→AGA) | yccS ← | putative transporter YccS |
| 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 |
| 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 | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| JC JC | 1,221,218 | IS3 (+) +3 bp | intergenic (+2017/+1085) | ymgF → / ← ymgD | inner membrane protein YmgF/PF16456 family protein YmgD |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | 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 |
| 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 | 1,419,679 | G→C | intergenic (‑223/+86) | ydaG ← / ← racR | uncharacterized protein YdaG/DNA‑binding transcriptional repressor RacR |
| RA | 1,456,421 | G→A | *166* (TGA→TAA) | paaD → | phenylacetate degradation protein |
| RA | 1,582,030 | A→C | T165T (ACT→ACG) | ydeN ← | putative sulfatase YdeN |
| 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 | 1,668,027 | C→A | E180* (GAG→TAG) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,951,320 | G→A | Q163Q (CAG→CAA) | yecD → | isochorismatase family protein YecD |
| RA | 1,951,332 | T→C | S167S (AGT→AGC) | yecD → | isochorismatase family protein YecD |
| RA | 1,951,335 | C→T | I168I (ATC→ATT) | yecD → | isochorismatase family protein YecD |
| RA | 1,951,338 | C→T | N169N (AAC→AAT) | yecD → | isochorismatase family protein YecD |
| RA | 1,986,220 | A→G | intergenic (‑92/‑705) | araF ← / → ftnB | arabinose ABC transporter periplasmic binding protein/putative ferritin‑like protein |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,043,522 | C→A | noncoding (36/90 nt) | serU ← | tRNA‑Ser |
| RA | 2,105,739 | T→A | S107C (AGT→TGT) | wbbI ← | beta‑1,6‑galactofuranosyltransferase WbbI |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,316,887 | G→A | intergenic (+60/+140) | rcsB → / ← rcsC | DNA‑binding transcriptional activator RcsB/histidine kinase RcsC |
| RA | 2,316,895 | G→A | intergenic (+68/+132) | rcsB → / ← rcsC | DNA‑binding transcriptional activator RcsB/histidine kinase RcsC |
| RA | 2,406,410 | C→T | A78T (GCC→ACC) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,867,332 | C→A | E74* (GAA→TAA) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,060,221 | G→A | D157N (GAT→AAT) | argP → | DNA‑binding transcriptional dual regulator ArgP |
| RA | 3,060,380 | G→T | D210Y (GAT→TAT) | argP → | DNA‑binding transcriptional dual regulator ArgP |
| MC JC | 3,096,674 | Δ33,472 bp | IS5‑mediated | rdgB–[yghO] | 30 genes rdgB, hemW, yggM, ansB, yggN, yggL, trmB, mutY, yggX, mltC, nupG, speC, yqgH, yqgA, pheV, yghD, yghE, yqhJ, yghF, yghG, pppA, yghJ, glcA, glcB, glcG, glcF, glcE, glcD, glcC, [yghO] |
| RA | 3,184,065 | A→T | P134P (CCT→CCA) | ribB ← | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,603,627 | G→T | T206N (ACC→AAC) | ftsY ← | signal recognition particle receptor |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| MC JC | 3,815,859 | Δ82 bp | [rph] | [rph] | |
| JC JC | 3,817,266 | IS3 (–) +4 bp :: +TC | coding (591‑594/864 nt) | yicC → | putative RNase adaptor protein YicC |
| RA | 3,837,039 | G→T | A29A (GCG→GCT) | setC → | putative arabinose exporter |
| RA | 3,844,617 | G→T | L218F (TTG→TTT) | adeD → | adenine deaminase |
| JC JC | 3,889,124 | IS5 (–) +4 bp | coding (395‑398/1416 nt) | tnaA → | tryptophanase |
| RA | 4,183,829 | T→C | L862P (CTC→CCC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,248,791 | G→A | G274D (GGT→GAT) | lamB → | maltose outer membrane channel/phage lambda receptor protein |
| RA | 4,283,161 | A→T | intergenic (‑86/+92) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,440,855 | G→A | P121S (CCG→TCG) | paeA ← | putative cadaverine/putrescine exporter |
| RA | 4,441,042 | A→T | F58L (TTT→TTA) | paeA ← | putative cadaverine/putrescine exporter |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,640,877 | G→T | intergenic (+106/‑65) | ytjE → / → yjtD | protein YtjE/putative tRNA/rRNA methyltransferase YjtD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196292 | 1211440 | 15149 | 22 [20] | [21] 22 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1962197 | 1979451 | 17255 | 117 [0] | [0] 109 | [yecT]–insA5 | [yecT],flhE,flhA,flhB,cheZ,cheY,cheB,cheR,tap,tar,cheW,cheA,cheA,motB,motA,motR,flhC,flhD,insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423908–3424233 | 3424440–3424238 | 6–533 | 22 [21] | [21] 22 | rrlD | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 87 (0.880) | 159 (1.610) | 37/594 | 1.2 | 63.9% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 93 (0.940) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 700754 = | 163 (1.640) | 513 (5.370) | 167/576 | 0.0 | 81.6% | coding (841/1221 nt) | nagC | DNA‑binding transcriptional dual regulator NagC |
| ? | NC_000913 | 1951242 = | 74 (0.770) | coding (411/567 nt) | yecD | isochorismatase family protein YecD | |||||
| * | ? | NC_000913 | = 1962196 | 0 (0.000) | 116 (1.170) | 78/596 | 0.1 | 100% | coding (225/489 nt) | yecT | protein YecT |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 108 (1.090) | 75/598 | 0.1 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979452 = | 0 (0.000) | intergenic (‑237/‑301) | insA5/uspC | IS1 family protein InsA/universal stress protein C | |||||