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 | freq | annotation | gene | description |
| RA | 32,767 | Δ1 bp | 5.6% | coding (1951/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 32,768 | Δ1 bp | 5.6% | coding (1952/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 202,875 | Δ1 bp | 6.3% | coding (316/789 nt) | lpxA → | UDP‑N‑acetylglucosamine acetyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 100% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 463,704 | Δ1 bp | 5.6% | coding (1790/1872 nt) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 463,705 | Δ1 bp | 5.6% | coding (1791/1872 nt) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 711,536 | C→T | 100% | intergenic (‑71/+69) | fldA ← / ← ybfE | flavodoxin 1/LexA‑regulated protein, CopB family |
| RA | 756,349 | C→T | 5.1% | T148M (ACG→ATG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 1,164,976 | G→A | 6.1% | P294P (CCG→CCA) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| JC JC | 1,259,760 | Δ1 bp :: IS186 (–) +5 bp | 39.6% | coding (1040‑1044/1680 nt) | dauA ← | C4‑dicarboxylic acid transporter |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,648,197 | A→T | 8.6% | K88N (AAA→AAT) | dicA → | Qin prophage; putative regulator for DicB |
| RA | 1,722,169 | A→G | 6.1% | T17A (ACG→GCG) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,304,537 | A→G | 14.0% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,459,579:1 | +G | 6.2% | coding (891/1311 nt) | fadI ← | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit |
| JC | 2,533,401 | Δ10 bp | 47.9% | intergenic (+21/‑354) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| RA | 2,759,640 | T→C | 10.3% | L219S (TTA→TCA) | yfjI → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,818,284 | C→T | 9.8% | intergenic (‑10/+189) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,288 | C→T | 9.8% | intergenic (‑14/+185) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,297 | A→T | 9.2% | intergenic (‑23/+176) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,303 | T→A | 8.9% | intergenic (‑29/+170) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,324 | G→A | 9.1% | intergenic (‑50/+149) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,819,349 | A→G | 6.3% | intergenic (‑203/+32) | csrA ← / ← alaS | pleiotropic regulatory protein for carbon source metabolism/alanyl‑tRNA synthetase |
| RA | 3,159,530 | G→A | 5.4% | G539G (GGC→GGT) | ygiQ ← | Radical SAM superfamily protein |
| JC | 3,213,570 | Δ48 bp | 45.7% | coding (524‑571/1842 nt) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| JC JC | 4,049,891 | IS5 (–) +4 bp | 91.0% | intergenic (+139/‑5) | polA → / → spf | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| RA | 4,076,022 | C→G | 5.9% | S157* (TCA→TGA) | yihX → | alpha‑D‑glucose‑1‑phosphate phosphatase, anomer‑specific |
| RA | 4,153,570 | G→A | 6.1% | intergenic (‑472/+126) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,595 | A→C | 7.7% | intergenic (‑497/+101) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,616 | C→T | 7.5% | intergenic (‑518/+80) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,246,255 | T→C | 7.0% | K55K (AAA→AAG) | malE ← | maltose transporter subunit |
| RA | 4,296,268 | T→C | 34.1% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 19.3% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,241 | C→T | 7.0% | intergenic (‑500/+158) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,247 | C→T | 9.0% | intergenic (‑506/+152) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,560,882 | A→T | 6.4% | intergenic (‑202/‑48) | yjiH ← / → kptA | nucleoside recognition pore and gate family putative inner membrane transporter/RNA 2'‑phosphotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423900–3424230 | 3424408–3424242 | 13–509 | 16 [15] | [15] 16 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4233739 | 4235454 | 1716 | 16 [15] | [15] 16 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 411642 = | 51 (0.900) | 3 (0.050) | 3/494 | NT | 6.0% | coding (840/1185 nt) | araJ | L‑arabinose‑inducible putative transporter, MFS family |
| ? | NC_000913 | 411680 = | 44 (0.800) | coding (802/1185 nt) | araJ | L‑arabinose‑inducible putative transporter, MFS family | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.260) | 31 (0.580) | 26/478 | NT | 68.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 14 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.260) | 33 (0.620) | 27/478 | NT | 70.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 14 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2729779 | 16 (0.280) | 4 (0.070) | 4/494 | NT | 20.5% | noncoding (1379/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 2730010 | NA (NA) | noncoding (1148/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 3714867 | 64 (1.120) | 4 (0.070) | 4/492 | NT | 6.6% | coding (1528/2334 nt) | bisC | biotin sulfoxide reductase |
| ? | NC_000913 | = 3715052 | 52 (0.950) | coding (1343/2334 nt) | bisC | biotin sulfoxide reductase | |||||
| * | ? | NC_000913 | 4317847 = | 77 (1.350) | 4 (0.070) | 4/490 | NT | 6.0% | coding (49/681 nt) | phnL | ribophosphonate triphosphate synthase subunit; putative ABC transporter‑related ATPase |
| ? | NC_000913 | 4318121 = | 51 (0.930) | coding (644/759 nt) | phnK | carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein | |||||