mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 18,794 | C→A | A27E (GCG→GAG) | nhaR → | DNA‑binding transcriptional activator NhaR |
| RA | 73,421 | C→A | A367A (GCG→GCT) | thiP ← | thiamine ABC transporter membrane subunit |
| RA | 79,984 | G→T | P294H (CCC→CAC) | leuC ← | 3‑isopropylmalate dehydratase subunit LeuC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 298,595 | C→A | V44V (GTG→GTT) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 304,730 | C→A | W159L (TGG→TTG) | ecpE ← | putative fimbrial chaperone EcpE |
| RA | 311,086 | G→T | A84E (GCG→GAG) | ecpR ← | DNA‑binding transcriptional dual regulator MatA |
| RA | 319,723 | G→T | D93E (GAC→GAA) | rclA ← | putative pyridine nucleotide‑disulfide oxidoreductase RclA |
| RA | 453,992 | G→T | A59E (GCA→GAA) | yajG ← | putative lipoprotein YajG |
| RA | 473,589 | G→T | V208V (GTG→GTT) | amtB → | ammonia/ammonium transporter |
| RA | 485,359 | G→T | I87I (ATC→ATA) | acrA ← | multidrug efflux pump membrane fusion lipoprotein AcrA |
| RA | 492,784 | G→T | Q231H (CAG→CAT) Q231H (CAG→CAT) |
dnaX → dnaX → |
DNA polymerase III subunit tau DNA polymerase III subunit tau |
| RA | 515,521 | C→A | A85S (GCC→TCC) | qmcA ← | PHB domain‑containing protein |
| RA | 591,492 | C→A | A563S (GCC→TCC) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 939,077 | G→T | E362* (GAA→TAA) | rarA → | recombination factor |
| RA | 1,018,313 | (T)6→5 | intergenic (‑14/‑172) | ycbZ ← / → matP | putative ATP‑dependent protease YcbZ/macrodomain Ter protein |
| RA | 1,022,546 | C→A | L446L (CTG→CTT) | yccS ← | putative transporter YccS |
| 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 | 1,282,225 | C→A | P788T (CCG→ACG) | narG → | nitrate reductase A subunit alpha |
| RA | 1,312,486 | G→T | I135I (ATC→ATA) | yciB ← | inner membrane protein |
| RA | 1,410,836 | G→T | Q442H (CAG→CAT) | dbpA → | ATP‑dependent RNA helicase DbpA |
| RA | 1,576,017 | G→T | L535M (CTG→ATG) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,661,966 | G→T | A471S (GCC→TCC) | ynfF → | putative selenate reductase YnfF |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,685,488 | G→C | H367Q (CAC→CAG) | fumC ← | fumarase C |
| RA | 1,686,761 | T→C | Q539Q (CAA→CAG) | fumA ← | fumarase A |
| RA | 1,691,454 | C→A | intergenic (+94/+132) | ydgA → / ← uidC | conserved protein YdgA/outer membrane porin family protein |
| RA | 1,829,660 | G→T | G25G (GGC→GGA) | astD ← | aldehyde dehydrogenase |
| RA | 1,836,628 | C→A | P186T (CCG→ACG) | ynjB → | putative ABC transporter periplasmic binding protein YnjB |
| 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 | 1,985,312 | C→A | G273C (GGT→TGT) | araF ← | arabinose ABC transporter periplasmic binding protein |
| RA | 2,138,179 | G→T | G93V (GGT→GTT) | yegH → | inner membrane protein YegH |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,193,875 | C→A | K98N (AAG→AAT) | mrp ← | P‑loop NTPase family protein |
| RA | 2,198,099 | C→A | intergenic (+801/‑2180) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,226,418 | C→A | intergenic (+39/+91) | yohD → / ← yohF | DedA family protein YohD/putative oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 2,228,669 | C→A | pseudogene (90/1436 nt) | mdtQ ← | putative multidrug resistance outer membrane protein MdtQ |
| RA | 2,246,117 | G→T | S218* (TCA→TAA) | cirA ← | ferric dihyroxybenzoylserine outer membrane transporter |
| RA | 2,352,173 | C→A | A68S (GCC→TCC) | glpT ← | sn‑glycerol 3‑phosphate:phosphate antiporter |
| RA | 2,359,636 | G→T | P173T (CCC→ACC) | yfaV ← | putative transporter YfaV |
| RA | 2,642,957 | G→C | intergenic (‑113/+172) | rodZ ← / ← rlmN | transmembrane component of cytoskeleton/23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase |
| RA | 2,672,080 | G→T | G12W (GGG→TGG) | hcaD → | putative 3‑phenylpropionate/cinnamate dioxygenase ferredoxin reductase subunit |
| RA | 2,674,680 | G→T | I3I (ATC→ATA) | yphB ← | putative aldose 1‑epimerase YphB |
| RA | 2,858,418 | C→A | G442G (GGC→GGA) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,926,893 | G→T | G196C (GGT→TGT) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,931,124 | C→A | P24T (CCC→ACC) | ygdG → | flap endonuclease |
| RA | 2,936,258 | C→A | A225A (GCC→GCA) | fucI → | L‑fucose isomerase |
| RA | 3,021,441 | G→T | G42G (GGG→GGT) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,029,329 | C→T | E535K (GAG→AAG) | ygfT ← | fused putative oxidoreductase, Fe‑S subunit and nucleotide‑binding subunit |
| RA | 3,145,797 | A→G | G155G (GGT→GGC) | hybO ← | hydrogenase 2 small subunit |
| RA | 3,211,299 | G→A | G65S (GGC→AGC) | dnaG → | DNA primase |
| RA | 3,254,160 | C→A | D19Y (GAT→TAT) | yhaJ ← | DNA‑binding transcriptional activator YhaJ |
| RA | 3,255,674 | C→A | T326T (ACG→ACT) | cyuA ← | putative L‑cysteine desulfidase CyuA |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,356,555 | C→A | L611M (CTG→ATG) | gltB → | glutamate synthase subunit GltB |
| RA | 3,390,203 | C→A | R228R (CGC→CGA) | aaeR → | LysR‑type transcriptional regulator AaeR |
| RA | 3,399,168 | C→A | G271W (GGG→TGG) | mreC ← | cell shape determining protein MreC |
| RA | 3,404,152 | G→T | V223V (GTG→GTT) | yhdH → | acrylyl‑CoA reductase |
| RA | 3,431,245 | C→A | G57G (GGG→GGT) | tsaC ← | threonylcarbamoyl‑AMP synthase |
| RA | 3,457,706 | G→T | A444S (GCC→TCC) | gspD → | Type II secretion system protein GspD |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,572,986 | C→A | G173C (GGC→TGC) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,724,026 | G→A | G124G (GGC→GGT) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,828,632 | C→A | A12S (GCC→TCC) | gltS ← | glutamate:sodium symporter |
| RA | 3,936,304 | G→T | L9L (CTG→CTT) | rbsB → | ribose ABC transporter periplasmic binding protein |
| RA | 3,936,872 | C→A | Q199K (CAG→AAG) | rbsB → | ribose ABC transporter periplasmic binding protein |
| RA | 4,022,591 | G→T | G125V (GGC→GTC) | tatB → | twin arginine protein translocation system ‑ TatB protein |
| RA | 4,219,183 | G→C | V196V (GTG→GTC) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,263,370 | C→A | A288S (GCC→TCC) | qorA ← | putative quinone oxidoreductase 1 |
| RA | 4,273,329 | G→T | G181G (GGC→GGA) | uvrA ← | excision nuclease subunit A |
| RA | 4,279,650 | G→T | G391V (GGT→GTT) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,365,091 | G→T | P89Q (CCG→CAG) | cutA ← | copper binding protein CutA |
| RA | 4,373,926 | C→A | L103L (CTG→CTT) | yjeJ ← | protein YjeJ |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196283 | 1211433 | 15151 | 23 [21] | [19] 22 | [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 | 3102950 | 3104090 | 1141 | 23 [20] | [21] 23 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3945673–3945905 | 3946127–3945916 | 12–455 | 22 [20] | [21] 22 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3363001 = | 128 (1.560) | 103 (1.270) | 48/276 | 0.3 | 61.1% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 89 (1.090) | 60/278 | 0.1 | 96.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||