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 | 70,659 | G→A | W91* (TGG→TGA) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 100,946 | T→C | M61T (ATG→ACG) | murC → | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| RA | 248,203 | G→A | intergenic (+69/‑2695) | rayT → / → dinB | REP‑associated tyrosine transposase/DNA polymerase IV |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 366,409 | C→T | intergenic (‑104/+19) | lacZ ← / ← lacI | beta‑galactosidase/DNA‑binding transcriptional repressor LacI |
| RA | 367,573 | G→A | intergenic (‑63/+14) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional activator MhpR |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 557,144 | C→A | V200L (GTA→TTA) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 690,948 | G→A | V279V (GTC→GTT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 1,069,743 | C→T | A33T (GCA→ACA) | rutG ← | pyrimidine:H(+) symporter |
| RA | 1,093,346 | (T)6→5 | coding (471/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,098,620 | T→A | V245V (GTT→GTA) | ghrA → | glyoxylate/hydroxypyruvate reductase A |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| 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 |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,304 | G→A | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| 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 | 1,310,770 | A→G | H32H (CAT→CAC) | yciI ← | protein YciI |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,357,202 | C→T | intergenic (‑92/+221) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,539,947 | C→G | A882P (GCG→CCG) | narZ ← | nitrate reductase Z subunit alpha |
| 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 | 1,728,754 | C→T | A136A (GCC→GCT) | rnt → | ribonuclease T |
| RA | 1,829,887 | G→A | A293A (GCC→GCT) | astA ← | arginine N‑succinyltransferase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,907,563 | IS1 (–) +9 bp | coding (21‑29/144 nt) | yobF ← | DUF2527 domain‑containing protein YobF |
| JC JC | 1,908,726 | IS2 (–) +5 bp | coding (37‑41/144 nt) | mgrB ← | PhoQ kinase inhibitor |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,042,171 | G→A | intergenic (+146/‑197) | zinT → / → yodB | metal‑binding protein ZinT/putative cytochrome b561 YodB |
| RA | 2,044,642 | T→C | intergenic (+18/‑296) | asnT → / → yeeJ | tRNA‑Asn/inverse autotransporter adhesin |
| 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 |
| JC JC | 2,175,525 | IS1 (+) +8 bp | coding (790‑797/1263 nt) | gatZ ← | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone |
| JC JC | 2,468,298 | IS3 (+) +3 bp | coding (85‑87/921 nt) | yfdH → | bactoprenol glucosyl transferase |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,661,908 | G→T | A75D (GCC→GAC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,867,454 | 2 bp→AA | coding (97‑98/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| JC JC | 2,916,218 | IS5 (–) +4 bp | coding (1162‑1165/2757 nt) | barA → | sensor histidine kinase BarA |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,939,297 | G→T | G137V (GGG→GTG) | fucU → | L‑fucose mutarotase |
| RA | 3,152,494 | G→T | A87S (GCG→TCG) | metC → | cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| JC JC | 3,350,556 | IS1 (–) +8 bp | intergenic (‑97/‑14) | elbB ← / → arcZ | low activity glyoxalase ElbB/small regulatory RNA ArcZ |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| JC JC | 3,429,986 | IS3 (–) +5 bp :: +T | coding (34‑38/258 nt) | yrdB ← | DUF1488 domain‑containing protein YrdB |
| RA | 3,553,662 | A→C | Q193P (CAG→CCG) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,443 | C→G | intergenic (+577/+179) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,669,782 | A→T | E64V (GAG→GTG) | treF → | cytoplasmic trehalase |
| RA | 3,707,878 | A→G | intergenic (‑173/+738) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,707,883 | G→A | intergenic (‑178/+733) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| 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 |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| JC JC | 3,888,869 | IS1 (+) +9 bp | coding (140‑148/1416 nt) | tnaA → | tryptophanase |
| RA | 4,212,973 | Δ1 bp | intergenic (+27/‑67) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 4,220,685 | A→G | F601F (TTT→TTC) | arpA ← | regulator of acetyl CoA synthetase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,287,464 | T→A | intergenic (‑93/‑147) | acs ← / → ytcB | acetyl‑CoA synthetase (AMP‑forming)/protein YtcB |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,475,493 | T→C | F19F (TTT→TTC) | yjgL → | protein YjgL |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| JC JC | 4,542,372 | IS1 (–) +9 bp | coding (336‑344/597 nt) | fimE → | regulator for fimA |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| 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 | 1196359 | 1211412 | 15054 | 4 [3] | [0] 6 | [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 | 2521130 | 2521220 | 91 | 14 [0] | [3] 4 | [valY] | [valY] |
| * | * | ÷ | NC_000913 | 2558699 | 2565482 | 6784 | 50 [0] | [3] 4 | intZ–[eutA] | intZ,yffL,yffM,yffN,yffO,yffP,yffQ,yffR,yffS,[eutA] |
| * | * | ÷ | NC_000913 | 3423898–3424423 | 3424423 | 1–526 | 4 [3] | [3] 4 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4035394–4035728 | 4036882–4035735 | 8–1489 | 4 [3] | [3] 4 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 256107 | 43 (0.900) | 43 (0.930) | 39/470 | 0.3 | 50.1% | coding (131/459 nt) | gpt | xanthine‑guanine phsophoribosyltransferase |
| ? | NC_000913 | 371382 = | 44 (0.960) | coding (144/867 nt) | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase | |||||
| * | ? | NC_000913 | 781577 = | 25 (0.520) | 14 (0.300) +G |
14/484 | 1.6 | 52.9% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521129 | 0 (0.000) | intergenic (+3/‑44) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 29 (0.620) | 27/478 | 0.6 | 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 | = 1978502 | 0 (0.000) | 22 (0.480) | 21/470 | 0.9 | 100% | intergenic (‑305/+16) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA5/uspC | IS1 family protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 2558698 | 0 (0.000) | 49 (1.060) | 45/470 | 0.2 | 100% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 0 (0.000) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | 4366825 = | 32 (0.670) | 17 (0.360) | 13/480 | 1.6 | 46.8% | intergenic (‑52/+14) | dcuA/aspX | C4‑dicarboxylate transporter DcuA/small regulatory RNA AspX |
| ? | NC_000913 | 4378238 = | 7 (0.150) | coding (707/1134 nt) | ampC | beta‑lactamase | |||||