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 | seq id | position | mutation | annotation | gene | description |
| RA | BN000925 | 9,791 | A→G | D797G (GAC→GGC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 9,802 | G→A | D801N (GAC→AAC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,089 | A→C | A896A (GCA→GCC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,359 | T→A | G986G (GGT→GGA) | tnpA → | Tn1 transposase |
| RA | BN000925 | 12,239 | +A | intergenic (‑601/+1055) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,406 | T→G | intergenic (‑768/+888) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,688 | T→A | intergenic (‑1050/+606) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 14,294 | G→C | G82A (GGC→GCC) | tetA → | tetracycline exporter protein |
| RA | BN000925 | 15,561 | Δ1 bp | intergenic (+312/+320) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,639 | C→G | intergenic (+390/+242) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,898 | +C | coding (649/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 16,410 | +T | coding (137/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 31,028 | C→G | P35A (CCC→GCC) | trbP → | TrbP protein |
| RA | BN000925 | 36,655 | A→G | R116G (AGA→GGA) R108G (AGA→GGA) |
istA → istA → |
IS21 transposase IS21 transposase |
| RA | BN000925 | 38,388 | A→C | pseudogene (45/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,390 | 1 bp→AG | pseudogene (47/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,393 | C→T | pseudogene (50/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,421 | Δ1 bp | pseudogene (78/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,510 | Δ1 bp | pseudogene (167/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,526 | Δ1 bp | intergenic (+12/‑232) | upf35.8 → / → aphA | probable truncation of theoretical product due to sequence errors/aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,136 | Δ1 bp | coding (379/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,147 | Δ1 bp | coding (390/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,179 | +CG | coding (422/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 49,066 | T→C | N542S (AAC→AGC) T29A (ACG→GCG) |
traI ← traH ← |
TraI DNA relaxase TraH protein |
| RA | BN000925 | 53,069 | +T | intergenic (+42/+10) | traM → / ← kfrC | TraM protein/KfrC protein |
| RA | BN000925 | 54,833 | Δ1 bp | intergenic (‑32/+127) | kfrB ← / ← kfrA | KfrB protein/KfrA coiled‑coil protein |
| RA | BN000925 | 56,817 | Δ1 bp | coding (297/522 nt) | korF ← | KorF repressor protein |
| RA | NC_000913 | 41,514 | A→G | F140L (TTC→CTC) | caiT ← | L‑carnitine:gamma‑butyrobetaine antiporter |
| RA | NC_000913 | 101,503 | A→G | T247A (ACC→GCC) | murC → | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
| RA | NC_000913 | 256,181 | C→T | R69C (CGC→TGC) | gpt → | xanthine‑guanine phsophoribosyltransferase |
| MC JC | NC_000913 | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | NC_000913 | 393,421 | C→T | pseudogene (452/1449 nt) | yaiT → | putative autotransporter YaiT |
| RA | NC_000913 | 423,318 | T→C | G267G (GGT→GGC) | malZ → | maltodextrin glucosidase |
| RA | NC_000913 | 451,047 | A→G | G188G (GGT→GGC) | cyoA ← | cytochrome bo3 ubiquinol oxidase subunit 2 |
| RA | NC_000913 | 485,714 | A→G | intergenic (‑95/‑47) | acrA ← / → acrR | multidrug efflux pump membrane fusion lipoprotein AcrA/DNA‑binding transcriptional repressor AcrR |
| RA | NC_000913 | 511,273 | A→G | V36A (GTG→GCG) V36A (GTG→GCG) |
copA ← copA ← |
Cu(+) exporting P‑type ATPase Cu(+) exporting P‑type ATPase |
| RA | NC_000913 | 566,565 | A→G | intergenic (‑204/‑119) | exoD ← / → renD | DLP12 prophage; putative exonuclease ExoD/DLP12 prophage; protein RenD |
| RA | NC_000913 | 603,924 | T→C | D247G (GAC→GGC) | ybdG ← | miniconductance mechanosensitive channel YbdG |
| RA | NC_000913 | 635,167 | T→C | P70P (CCA→CCG) | ybdM ← | ParB‑like nuclease domain‑containing protein YbdM |
| RA | NC_000913 | 777,169 | A→G | A276A (GCA→GCG) | tolA → | Tol‑Pal system protein TolA |
| RA | NC_000913 | 956,316 | (T)5→4 | coding (317/1761 nt) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| JC JC | NC_000913 | 986,536 | IS1 (–) +9 bp | coding (439‑447/1089 nt) | ompF ← | outer membrane porin F |
| RA | NC_000913 | 1,002,888 | T→C | intergenic (+11/‑1) | elfG → / → ycbU | putative fimbrial‑like adhesin protein/putative fimbrial protein YcbU |
| RA | NC_000913 | 1,038,874 | G→A | A379T (GCG→ACG) | appC → | cytochrome bd‑II ubiquinol oxidase subunit I |
| RA | NC_000913 | 1,071,519 | C→T | A83T (GCA→ACA) | rutD ← | putative aminoacrylate hydrolase |
| RA | NC_000913 | 1,074,537 | G→A | R99H (CGT→CAT) | rutR → | DNA‑binding transcriptional dual regulator RutR |
| RA | NC_000913 | 1,125,819 | (A)5→4 | coding (258/585 nt) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | NC_000913 | 1,233,315 | C→T | R468H (CGC→CAC) | nhaB ← | Na(+):H(+) antiporter NhaB |
| RA | NC_000913 | 1,258,868 | +G | coding (78/279 nt) | ychH → | stress‑induced protein |
| RA | NC_000913 | 1,259,472 | A→G | R444R (CGT→CGC) | dauA ← | aerobic C4‑dicarboxylate transporter DauA |
| RA | NC_000913 | 1,296,380 | T→C | Y581C (TAC→TGC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | NC_000913 | 1,306,311 | C→T | P183L (CCG→CTG) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | NC_000913 | 1,341,897 | G→A | intergenic (+170/‑24) | lapB → / → pyrF | lipopolysaccharide assembly protein B/orotidine‑5'‑phosphate decarboxylase |
| RA | NC_000913 | 1,348,200 | C→T | G238D (GGC→GAC) | rnb ← | RNase II |
| RA | NC_000913 | 1,376,731 | A→G | Y233C (TAT→TGT) | ycjR → | putative ketohexose‑3‑epimerase YcjR |
| RA | NC_000913 | 1,423,531 | (C)6→7 | pseudogene (187/300 nt) coding (132/186 nt) |
rzpR → rzoR → |
Rac prophage; putative endopeptidase RzpR Rac prophage; putative lipoprotein |
| RA | NC_000913 | 1,453,738 | T→A | intergenic (‑96/‑189) | paaZ ← / → paaA | oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase/phenylacetyl‑CoA 1,2‑epoxidase, monooxygenase subunit |
| RA | NC_000913 | 1,596,247 | T→C | pseudogene (1840/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | NC_000913 | 1,697,592 | T→A | E150V (GAA→GTA) | hdhA ← | 7‑alpha‑hydroxysteroid dehydrogenase |
| RA | NC_000913 | 1,890,139 | T→C | T132A (ACG→GCG) | yeaY ← | Slp family lipoprotein YeaY |
| RA | NC_000913 | 1,923,946 | (G)6→7 | coding (646/873 nt) | yebZ ← | putative inner membrane protein |
| RA | NC_000913 | 1,980,208 | T→C | T469A (ACC→GCC) | otsA ← | trehalose‑6‑phosphate synthase |
| RA | NC_000913 | 2,017,429 | (C)6→7 | coding (876/1374 nt) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | NC_000913 | 2,077,077 | A→G | intergenic (+39/‑35) | yeeT → / → cbeA | CP4‑44 prophage; DUF987 domain‑containing protein YeeT/CP4‑44 prophage; cytoskeleton bundling‑enhancing antitoxin CbeA |
| RA | NC_000913 | 2,089,450 | A→G | S6P (TCT→CCT) | yoeB ← | ribosome‑dependent mRNA interferase toxin YoeB |
| RA | NC_000913 | 2,091,063 | T→C | V291A (GTC→GCC) | hisG → | ATP phosphoribosyltransferase |
| RA | NC_000913 | 2,146,947 | T→C | I198M (ATA→ATG) | alkA ← | DNA‑3‑methyladenine glycosylase 2 |
| RA | NC_000913 | 2,151,352 | (A)6→7 | coding (168/462 nt) | yegJ → | DUF2314 domain‑containing protein YegJ |
| RA | NC_000913 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | NC_000913 | 2,187,135 | A→G | Y59C (TAC→TGC) | rcnB → | periplasmic protein involved in nickel/cobalt export |
| RA | NC_000913 | 2,249,394 | T→C | E75E (GAA→GAG) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | NC_000913 | 2,249,587 | A→T | F11Y (TTT→TAT) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | NC_000913 | 2,371,703 | G→A | A266T (GCC→ACC) | arnT → | lipid IVA 4‑amino‑4‑deoxy‑L‑arabinosyltransferase |
| RA | NC_000913 | 2,677,417 | T→C | E315E (GAA→GAG) | yphE ← | putative ABC transporter ATP‑binding protein YphE |
| RA | NC_000913 | 2,803,041 | T→C | M565T (ATG→ACG) | nrdE → | ribonucleoside‑diphosphate reductase 2 subunit alpha |
| RA | NC_000913 | 2,830,033 | T→C | V74A (GTC→GCC) | gutQ → | D‑arabinose 5‑phosphate isomerase GutQ |
| RA | NC_000913 | 2,858,471 | T→G | L460R (CTG→CGG) | mutS → | DNA mismatch repair protein MutS |
| RA | NC_000913 | 2,909,089 | T→C | H193R (CAC→CGC) | pyrG ← | CTP synthetase |
| RA | NC_000913 | 2,912,294 | T→C | Y453C (TAC→TGC) | relA ← | GDP/GTP pyrophosphokinase |
| RA | NC_000913 | 3,082,691 | T→C | intergenic (+20/+186) | loiP → / ← speB | metalloprotease LoiP/agmatinase |
| RA | NC_000913 | 3,121,626 | (T)6→5 | intergenic (‑347/+8) | glcA ← / ← glcB | glycolate/lactate:H(+) symporter GlcA/malate synthase G |
| RA | NC_000913 | 3,125,235 | G→A | C75C (TGC→TGT) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
| RA | NC_000913 | 3,143,821 | T→C | N115S (AAC→AGC) | hybB ← | hydrogenase 2 membrane subunit |
| RA | NC_000913 | 3,145,905 | A→G | G119G (GGT→GGC) | hybO ← | hydrogenase 2 small subunit |
| RA | NC_000913 | 3,149,505 | T→C | intergenic (‑34/‑157) | yqhA ← / → yghA | uncharacterized protein YqhA/NADP(+)‑dependent aldehyde reductase |
| RA | NC_000913 | 3,215,335 | T→C | T47A (ACC→GCC) | mug ← | stationary phase mismatch/uracil DNA glycosylase |
| MC JC | NC_000913 | 3,366,751 | Δ295 bp | IS5‑mediated | yhcE–[yhcF] | yhcE, [yhcF] |
| RA | NC_000913 | 3,372,618 | A→G | intergenic (‑44/+65) | nanT ← / ← nanA | N‑acetylneuraminate:H(+) symporter/N‑acetylneuraminate lyase |
| RA | NC_000913 | 3,389,809 | G→A | G97D (GGC→GAC) | aaeR → | LysR‑type transcriptional regulator AaeR |
| RA | NC_000913 | 3,416,456 | T→C | V475A (GTT→GCT) | acrF → | multidrug efflux pump RND permease AcrF |
| RA | NC_000913 | 3,468,945 | A→G | G303G (GGT→GGC) | chiA ← | endochitinase |
| RA | NC_000913 | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | NC_000913 | 3,671,805 | (C)5→6 | coding (90/603 nt) | yhjB ← | putative DNA‑binding transcriptional regulator YhjB |
| RA | NC_000913 | 3,717,751 | C→T | L148L (CTG→TTG) | ghrB → | glyoxylate reductase |
| RA | NC_000913 | 3,736,430 | T→C | T250A (ACC→GCC) | bax ← | putative glycoside hydrolase Bax |
| RA | NC_000913 | 3,773,041 | (G)6→7 | coding (761/1914 nt) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | NC_000913 | 3,836,534 | (C)6→7 | intergenic (+218/‑419) | selC → / → setC | tRNA‑Sec/putative arabinose exporter |
| RA | NC_000913 | 3,913,700 | T→C | intergenic (‑32/+130) | glmS ← / ← glmU | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase/fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase |
| RA | NC_000913 | 3,925,397 | G→A | I79I (ATC→ATT) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | NC_000913 | 4,045,148 | A→G | H317R (CAC→CGC) | yihF → | uncharacterized protein YihF |
| RA | NC_000913 | 4,212,959 | G→C | intergenic (+13/‑81) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,212,973 | Δ1 bp | intergenic (+27/‑67) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,252,763 | A→G | E86E (GAA→GAG) | ubiC → | chorismate lyase |
| RA | NC_000913 | 4,285,058 | G→T | G52G (GGC→GGA) | yjcH ← | conserved inner membrane protein YjcH |
| RA | NC_000913 | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | NC_000913 | 4,370,387 | C→T | G9E (GGG→GAG) | yjeH ← | L‑methionine/branched chain amino acid exporter |
| RA | NC_000913 | 4,482,686 | C→T | V384V (GTG→GTA) | valS ← | valine‑‑tRNA ligase |
| RA | NC_000913 | 4,523,716 | T→C | T127A (ACG→GCG) | yjhG ← | KpLE2 phage‑like element; D‑xylonate dehydratase |
| RA | NC_000913 | 4,571,392 | A→G | R61R (CGT→CGC) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | NC_000913 | 4,603,521 | A→G | I15M (ATA→ATG) | yjjQ → | DNA‑binding transcriptional repressor YjjQ |
| RA | NC_000913 | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | NC_000913 | 4,618,967 | G→A | A247T (GCC→ACC) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423830–3424234 | 3424464–3424241 | 8–635 | 33 [32] | [32] 33 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 68 (0.700) +G |
37/428 | 1.7 | 58.0% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | = 4171849 | 99 (1.010) | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 1207790 = | 29 (0.300) | 106 (1.170) | 63/398 | 0.2 | 79.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 29 (0.320) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.300) | 85 (0.930) | 59/398 | 0.3 | 75.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 29 (0.320) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 88 (0.910) | 59/422 | 0.4 | 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 | |||||