mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 527,354 | A→T | 8.7% | D1365V (GAT→GTT) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 724,131 | A→G | 6.4% | L95P (CTC→CCC) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| 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 | 1,678,024 | C→T | 100% | intergenic (‑121/‑403) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein |
| RA | 1,697,375 | T→C | 100% | Q222Q (CAA→CAG) | hdhA ← | 7‑alpha‑hydroxysteroid dehydrogenase, NAD‑dependent |
| 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 | 2,817,875 | T→C | 7.2% | intergenic (‑15/+184) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,877 | C→T | 7.2% | intergenic (‑17/+182) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,884 | T→A | 8.0% | intergenic (‑24/+175) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,886:1 | +T | 6.4% | intergenic (‑26/+173) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,886:2 | +T | 6.4% | intergenic (‑26/+173) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,888 | A→T | 8.7% | intergenic (‑28/+171) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 3,394,830 | Δ1 bp | 5.1% | coding (1429/3801 nt) | yhdP ← | DUF3971‑AsmA2 domains protein |
| 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 |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 8.7% | intergenic (+266/+376) | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583130 | 583863 | 734 | 32 [28] | [28] 30 | [tfaX]–[appY] | [tfaX],[appY] |
| * | * | ÷ | NC_000913 | 1465068 | 1465390 | 323 | 32 [29] | [29] 31 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 1978500 | 1979278 | 779 | 30 [29] | [6] 35 | insB1–insA | insB1,insA |
| * | * | ÷ | NC_000913 | 2099734 | 2101366 | 1633 | 30 [28] | [24] 31 | gnd | gnd |
| * | * | ÷ | NC_000913 | 2455651 | 2456228 | 578 | 30 [26] | [27] 31 | yfcV/sixA | putative fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| * | * | ÷ | NC_000913 | 2990601 | 2991477 | 877 | 30 [28] | [28] 32 | [ygeF]–[ygeG] | [ygeF],ygeF,[ygeG] |
| * | * | ÷ | NC_000913 | 3499273 | 3499505 | 233 | 31 [28] | [28] 30 | [yhfL] | [yhfL] |
| * | * | ÷ | NC_000913 | 3769501 | 3770108 | 608 | 33 [29] | [29] 30 | [yibV]–[yibU] | [yibV],yibV,yibU,[yibU] |
| * | * | ÷ | NC_000913 | 3798606 | 3799517 | 912 | 30 [28] | [17] 34 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 3804153 | 3805223 | 1071 | 33 [27] | [29] 32 | waaS–[waaP] | waaS,[waaP] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 825508 | 98 (1.150) | 5 (0.060) | 5/488 | NT | 5.3% | coding (601/1107 nt) | ybhR | putative ABC transporter permease |
| ? | NC_000913 | = 825997 | 83 (1.000) | coding (112/1107 nt) | ybhR | putative ABC transporter permease | |||||
| * | ? | NC_000913 | 1207790 = | 28 (0.330) | 53 (0.670) | 48/466 | NT | 67.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.300) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.320) | 50 (0.630) | 40/466 | NT | 67.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.300) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1387098 | 86 (1.010) | 10 (0.120) | 6/486 | NT | 10.3% | coding (379/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| ? | NC_000913 | = 1387248 | 90 (1.080) | coding (529/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase | |||||
| * | ? | NC_000913 | 1756151 = | 75 (0.880) | 4 (0.050) | 4/480 | NT | 5.1% | coding (454/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913 | 1756478 = | 77 (0.940) | coding (781/1413 nt) | pykF | pyruvate kinase I | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 28 (0.340) | 24/482 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 3567579 | 47 (0.550) | 4 (0.050) | 4/476 | NT | 6.8% | coding (455/1434 nt) | glgA | glycogen synthase |
| ? | NC_000913 | = 3567837 | 64 (0.790) | coding (197/1434 nt) | glgA | glycogen synthase | |||||
| * | ? | NC_000913 | = 3951734 | 6 (0.070) | 80 (0.970) | 57/482 | NT | 93.7% | pseudogene (193/663 nt) | ilvG | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| ? | NC_000913 | 3952061 = | 5 (0.060) | pseudogene (520/663 nt) | ilvG | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted | |||||