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 | 33,448 | G→A | G878S (GGC→AGC) | carB → | carbamoyl‑phosphate synthetase large subunit |
| RA | 38,632 | G→A | P162S (CCT→TCT) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 60,007 | G→A | P114S (CCG→TCG) | rluA ← | 23S rRNA pseudouridine(746) and tRNA pseudouridine(32) synthase |
| RA | 82,494 | A→C | Y346D (TAT→GAT) | leuA ← | 2‑isopropylmalate synthase |
| RA | 85,004 | G→A | A213T (GCG→ACG) | leuO → | DNA‑binding transcriptional dual regulator LeuO |
| RA | 87,278 | G→A | S550N (AGC→AAC) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 94,970 | G→A | G107G (GGG→GGA) | murF → | D‑alanyl‑D‑alanine‑adding enzyme |
| RA | 95,733 | G→A | A362T (GCG→ACG) | murF → | D‑alanyl‑D‑alanine‑adding enzyme |
| RA | 151,033 | G→A | S189S (AGC→AGT) | yadK ← | putative fimbrial protein YadK |
| RA | 161,553 | G→A | A160V (GCC→GTC) | thpR ← | RNA 2',3'‑cyclic phosphodiesterase |
| RA | 172,988 | G→A | L509L (CTG→CTA) | fhuB → | iron(III) hydroxamate ABC transporter membrane subunit |
| RA | 182,975 | C→T | V171V (GTC→GTT) | cdaR → | DNA‑binding transcriptional activator CdaR |
| RA | 199,860 | G→A | E645K (GAG→AAG) | bamA → | outer membrane protein assembly factor BamA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 279,802 | G→A | A25V (GCC→GTC) | insA2 ← | IS1 family protein InsA |
| RA | 284,709 | G→A | G503G (GGG→GGA) | yagF → | D‑xylonate dehydratase |
| RA | 285,196 | G→A | intergenic (+28/‑199) | yagF → / → yagG | D‑xylonate dehydratase/putative D‑xylonate transporter YagG |
| RA | 288,170 | G→A | S461N (AGC→AAC) | yagH → | putative xylosidase/arabinosidase |
| RA | 458,316 | G→A | K297K (AAG→AAA) | clpX → | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | 559,893 | G→A | G66D (GGC→GAC) | sfmD → | putative fimbrial usher protein SfmD |
| MC JC | 574,454 | Δ137 bp | IS5‑mediated | nmpC | nmpC |
| RA | 864,722 | A→G | N136N (AAT→AAC) | moeB ← | molybdopterin‑synthase adenylyltransferase |
| RA | 1,093,359 | C→G | P162A (CCG→GCG) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,180,048 | T→G | C177G (TGC→GGC) C177G (TGC→GGC) |
cobB → cobB → |
protein‑lysine deacetylase/desuccinylase/lipoamidase protein‑lysine deacetylase/desuccinylase/lipoamidase |
| JC JC | 1,230,017 | IS2 (–) +5 bp | coding (374‑378/912 nt) | hlyE ← | hemolysin E |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,381,086 | C→T | intergenic (+279/‑861) | ycjU → / → ompG | beta‑phosphoglucomutase/outer membrane porin G |
| RA | 1,400,600 | C→T | A392T (GCG→ACG) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| RA | 1,421,263 | C→T | L49L (CTG→TTG) | ydaU → | DUF1376 domain‑containing protein YdaU |
| RA | 1,423,344 | G→A | intergenic (+32/‑56) | ydaW → / → rzoR | putative uncharacterized protein YdaW/putative prophage outer membrane lipoprotein RzoR |
| RA | 1,516,393 | C→T | G272G (GGC→GGT) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,524,975 | C→T | G336S (GGC→AGC) | ansP ← | L‑asparagine transporter |
| RA | 1,528,004 | C→T | intergenic (+852/‑1918) | yncH → / → ydcD | DUF5445 domain‑containing protein YncH/uncharacterized protein YdcD |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,668,262 | IS2 (–) +5 bp | coding (299‑303/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,039,654 | (C)5→6 | coding (177/1005 nt) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,107,809 | C→T | R174K (AGA→AAA) | glf ← | UDP‑galactopyranose mutase |
| RA | 2,144,034 | C→T | L257F (CTT→TTT) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,149,988 | C→T | G333D (GGT→GAT) | yegI ← | putative serine/threonine‑protein kinase YegI |
| RA | 2,159,187 | G→C | D268H (GAT→CAT) | mdtC → | multidrug efflux pump RND permease subunit MdtC |
| RA | 2,165,412 | A→T | H75L (CAT→CTT) | yegP → | DUF1508 domain‑containing protein YegP |
| MC JC | 2,171,429 | Δ6,547 bp | IS3‑mediated | [gatR]–[fbaB] | [gatR], gatD, gatB, gatA, gatZ, gatY, [fbaB] |
| RA | 2,197,779 | C→T | intergenic (+481/‑2500) | yehF → / → yehI | PF05406 family protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,216,654 | C→T | D252N (GAT→AAT) | yehX ← | glycine betaine ABC transporter ATP binding subunit YehX |
| RA | 2,260,023 | C→T | G463D (GGC→GAC) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,261,163 | C→T | G83D (GGC→GAC) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,267,551 | G→A | S436N (AGC→AAC) | yeiQ → | putative oxidoreductase YeiQ |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,456,751 | C→A | R21L (CGT→CTT) | sixA ← | phosphohistidine phosphatase SixA |
| RA | 2,861,081 | C→T | V52M (GTG→ATG) | ygbI ← | DNA‑binding transcriptional repressor YgbI |
| RA | 2,867,455 | G→C | Q33E (CAG→GAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,882,934 | C→T | G402E (GGG→GAG) | casA ← | type I‑E CRISPR system Cascade subunit CasA |
| RA | 2,950,012 | C→T | A257A (GCC→GCT) | argA → | N‑acetylglutamate synthase |
| RA | 2,964,821 | A→G | I112T (ATC→ACC) | thyA ← | thymidylate synthase |
| RA | 2,967,599 | A→T | F279Y (TTT→TAT) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,990,250 | C→T | E37E (GAG→GAA) | yqeK ← | protein YqeK |
| RA | 3,022,584 | C→T | V423V (GTC→GTT) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,023,159 | C→T | S615F (TCC→TTC) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,028,355 | C→T | T412I (ACC→ATC) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| RA | 3,031,244 | C→T | intergenic (‑313/‑123) | ygfT ← / → uacT | putative oxidoreductase YgfT/urate:H(+) symporter |
| RA | 3,038,813 | C→T | G4S (GGT→AGT) | dsbC ← | protein disulfide isomerase DsbC |
| RA | 3,051,427 | C→T | L297L (CTG→CTA) | ubiI ← | 2‑octaprenylphenol 6‑hydroxylase |
| RA | 3,055,383 | C→T | G21E (GGG→GAG) | ygfB ← | PF03695 family protein YgfB |
| RA | 3,061,803 | C→T | C318C (TGC→TGT) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,092,276 | C→T | D133D (GAC→GAT) | gshB → | glutathione synthetase |
| RA | 3,111,071 | C→T | S19N (AGC→AAC) | yghD ← | putative type II secretion system M‑type protein YghD |
| RA | 3,116,060 | C→T | G1018D (GGC→GAC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,125,729 | C→T | S265N (AGT→AAT) | glcE ← | glycolate dehydrogenase, putative FAD‑binding subunit |
| RA | 3,137,964 | C→T | G187S (GGC→AGC) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,142,761 | C→T | E77K (GAA→AAA) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,148,786 | C→T | S297L (TCG→TTG) | gpr → | L‑glyceraldehyde 3‑phosphate reductase |
| RA | 3,176,283 | C→T | G184D (GGC→GAC) | cpdA ← | cAMP phosphodiesterase |
| RA | 3,195,554 | C→T | L400L (CTG→CTA) | hldE ← | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase |
| RA | 3,200,748 | C→T | R73K (AGA→AAA) | ygiF ← | inorganic triphosphatase |
| RA | 3,215,594 | C→T | intergenic (‑121/‑4) | mug ← / → ileX | stationary phase mismatch/uracil DNA glycosylase/tRNA‑Ile |
| RA | 3,215,671 | C→T | noncoding (74/76 nt) | ileX → | tRNA‑Ile |
| RA | 3,239,705 | C→T | intergenic (+160/‑239) | alx → / → sstT | putative membrane‑bound redox modulator Alx/serine/threonine:Na(+) symporter |
| RA | 3,248,851 | C→T | intergenic (+29/‑118) | mzrA → / → yqjC | modulator protein MzrA/DUF1090 domain‑containing protein YqjC |
| RA | 3,268,718 | G→A | D102N (GAC→AAC) | yhaC → | uncharacterized protein YhaC |
| RA | 3,308,639 | G→A | P96S (CCT→TCT) | nlpI ← | lipoprotein NlpI |
| RA | 3,317,041 | G→A | I162I (ATC→ATT) | nusA ← | transcription termination/antitermination protein NusA |
| RA | 3,354,491 | T→G | intergenic (‑441/‑234) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,474,425 | T→G | K43T (AAA→ACA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,533,224 | G→C | R136P (CGT→CCT) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,549,226 | C→T | R282H (CGC→CAC) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,582,125 | Δ1,303 bp | IS1‑mediated | [yhhZ]–[yrhA] | [yhhZ], [yrhA] |
| RA | 3,942,092 | C→T | noncoding (285/1542 nt) | rrsC → | 16S ribosomal RNA |
| JC JC | 3,948,343 | IS2 (–) +5 bp | coding (258‑262/339 nt) | maoP → | macrodomain Ori protein |
| RA | 4,038,529 | G→A | noncoding (1011/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,103,889 | G→A | R363C (CGT→TGT) | cpxA ← | sensor histidine kinase CpxA |
| RA | 4,115,937 | G→A | T429I (ACC→ATC) | glpK ← | glycerol kinase |
| RA | 4,183,786 | G→A | E848K (GAA→AAA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,467,310 | G→A | intergenic (‑64/‑121) | treR ← / → mgtL | DNA‑binding transcriptional repressor TreR/leader peptide MgtL |
| RA | 4,468,660 | G→A | V346I (GTA→ATA) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,471,869 | G→A | A176V (GCG→GTG) | pyrB ← | aspartate carbamoyltransferase catalytic subunit |
| RA | 4,479,787 | A→G | T20A (ACA→GCA) | yjgN → | inner membrane protein YjgN |
| RA | 4,492,454 | G→A | G24G (GGC→GGT) | idnT ← | L‑idonate/5‑ketogluconate/gluconate transporter |
| RA | 4,500,990 | G→A | intergenic (+1490/‑270) | insD6 → / → yjgZ | IS2 insertion element protein InsB/uncharacterized protein YjgZ |
| RA | 4,507,161 | G→A | intergenic (+588/‑36) | ythA → / → insO | uncharacterized protein YthA/IS911B regulator fragment |
| RA | 4,509,571 | C→T | pseudogene (93/315 nt) | insO → | IS911B regulator fragment |
| RA | 4,518,426 | G→A | V19I (GTC→ATC) | ykiE → | protein YkiE |
| RA | 4,520,172 | G→A | A51A (GCC→GCT) | yjhU ← | putative DNA‑binding transcriptional regulator YjhU |
| RA | 4,522,864 | G→A | L411F (CTC→TTC) | yjhG ← | D‑xylonate dehydratase |
| RA | 4,531,353 | G→A | S100F (TCC→TTC) | sgcX ← | putative endoglucanase with Zn‑dependent exopeptidase domain |
| RA | 4,532,864 | G→A | A107V (GCG→GTG) | yjhP ← | putative methyltransferase YjhP |
| RA | 4,543,654 | G→A | Q180Q (CAG→CAA) | fimA → | type 1 fimbriae major subunit |
| RA | 4,551,644 | G→A | Q3Q (CAG→CAA) | uxuA → | D‑mannonate dehydratase |
| RA | 4,556,867 | G→A | intergenic (+70/‑46) | ytiD → / → idlP | protein YtiD/iraD leader peptide |
| RA | 4,562,404 | G→A | A91V (GCG→GTG) | yjiJ ← | putative transporter YjiJ |
| RA | 4,570,961 | G→A | S205L (TCG→TTG) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,583,948 | G→A | N938N (AAC→AAT) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,590,986 | G→A | I98I (ATC→ATT) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,600,647 | G→A | T110I (ACC→ATC) | dnaC ← | DNA replication protein DnaC |
| RA | 4,610,488 | G→A | A359T (GCG→ACG) | prfC → | peptide chain release factor RF3 |
| JC | 4,617,562 | (CAACTTCCCACACGGTAAC)1→2 | coding (240/780 nt) | deoC → | deoxyribose‑phosphate aldolase |
| RA | 4,625,303 | G→A | G137S (GGC→AGC) | serB → | phosphoserine phosphatase |
| RA | 4,630,742 | G→A | A4T (GCC→ACC) | slt → | soluble lytic murein transglycosylase |
| RA | 4,631,251 | G→A | W173* (TGG→TGA) | slt → | soluble lytic murein transglycosylase |
| RA | 4,632,689 | G→A | intergenic (+19/‑71) | slt → / → trpR | soluble lytic murein transglycosylase/DNA‑binding transcriptional repressor TrpR |
| RA | 4,637,813 | G→A | G373E (GGA→GAA) | creC → | sensory histidine kinase CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423909–3424233 | 3424444–3424238 | 6–536 | 28 [24] | [25] 26 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3515198 | 3515801 | 604 | 26 [25] | [25] 26 | dam | DNA adenine methyltransferase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 18 (0.170) | 54 (0.530) | 41/566 | 1.1 | 68.3% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 33 (0.330) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 20 (0.190) | 49 (0.480) | 40/566 | 1.2 | 65.4% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 33 (0.330) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 118 (1.120) | 78/590 | 0.1 | 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 | 3583428 = | NA (NA) | 191 (1.780) | 106/598 | 0.0 | 58.8% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4599508 = | 134 (1.250) | intergenic (‑67/+187) | opgB/yjjA | phosphoglycerol transferase I/DUF2501 domain‑containing protein YjjA | |||||