mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 120,459 | Δ1 bp | 3.3% | coding (1093/1374 nt) | aroP ← | aromatic amino acid transporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 317,069:1 | +G | 4.5% | pseudogene (101/684 nt) | ykgA ← | pseudogene, AraC family,putative regulator, Not classified, putative ARAC‑type regulatory protein |
| 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 | 601,507 | G→T | 4.8% | A932S (GCC→TCC) | cusA → | copper/silver efflux system, membrane component |
| RA | 613,679 | G→A | 4.2% | G315R (GGG→AGG) | fes → | enterobactin/ferrienterobactin esterase |
| RA | 724,131 | A→G | 6.3% | L95P (CTC→CCC) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 799,615 | Δ1 bp | 5.0% | intergenic (+34/+7) | pgl → / ← ybhD | 6‑phosphogluconolactonase/putative DNA‑binding transcriptional regulator |
| RA | 1,046,106 | C→T | 4.7% | A614T (GCC→ACC) | gfcD ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,096,121 | A→T | 4.7% | T93T (ACA→ACT) | ycdU → | putative inner membrane protein |
| RA | 1,136,717 | C→G | 3.7% | A148A (GCC→GCG) | flgI → | putative flagellar basal body protein |
| 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 | 1,309,004 | C→T | 4.1% | intergenic (+43/+12) | yciY → / ← kch | uncharacterized protein/voltage‑gated potassium channel |
| RA | 1,547,029 | Δ1 bp | 4.8% | coding (141/882 nt) | yddG ← | aromatic amino acid exporter |
| RA | 1,547,030 | Δ1 bp | 4.9% | coding (140/882 nt) | yddG ← | aromatic amino acid exporter |
| RA | 1,547,031 | Δ1 bp | 4.9% | coding (139/882 nt) | yddG ← | aromatic amino acid exporter |
| 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 |
| RA | 1,708,930 | C→A | 11.8% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,436,489 | T→C | 3.7% | T53T (ACA→ACG) | usg ← | putative semialdehyde dehydrogenase |
| RA | 2,817,873 | T→C | 7.0% | intergenic (‑15/+184) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,875 | C→T | 9.9% | intergenic (‑17/+182) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,882 | T→A | 7.8% | intergenic (‑24/+175) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,885:1 | +T | 6.2% | intergenic (‑27/+172) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,885:2 | +T | 6.2% | intergenic (‑27/+172) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,886 | A→T | 9.6% | intergenic (‑28/+171) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,907 | A→G | 4.9% | intergenic (‑49/+150) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,914 | T→G | 4.5% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 3,292,235 | G→A | 3.6% | V299V (GTG→GTA) | yraK → | putative fimbrial‑like adhesin protein |
| RA | 3,377,053 | Δ1 bp | 3.1% | coding (366/639 nt) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,377,054 | Δ1 bp | 3.1% | coding (365/639 nt) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,377,055 | Δ1 bp | 3.1% | coding (364/639 nt) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,377,056 | Δ1 bp | 3.1% | coding (363/639 nt) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,377,057 | Δ1 bp | 3.1% | coding (362/639 nt) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,377,058 | Δ1 bp | 3.1% | coding (361/639 nt) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,377,059 | Δ1 bp | 3.1% | coding (360/639 nt) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,394,828 | Δ1 bp | 5.1% | coding (1429/3801 nt) | yhdP ← | DUF3971‑AsmA2 domains protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,921,103 | C→T | 4.8% | G29D (GGC→GAC) | atpE ← | F0 sector of membrane‑bound ATP synthase, subunit c |
| RA | 3,994,528 | A→G | 4.2% | N3S (AAC→AGC) | yifL → | putative lipoprotein |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,161,004 | A→G | 4.4% | intergenic (‑215/‑119) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,201,235 | G→A | 4.2% | W224* (TGG→TAG) | yjaH → | DUF1481 family putative lipoprotein |
| RA | 4,449,800 | C→T | 3.8% | intergenic (‑147/‑163) | ppa ← / → ytfQ | inorganic pyrophosphatase/galactofuranose ABC transporter periplasmic binding 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] | [8] 37 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2099734 | 2101366 | 1633 | 30 [28] | [25] 32 | gnd | gnd |
| * | * | ÷ | NC_000913 | 2455649 | 2456226 | 578 | 30 [26] | [27] 31 | yfcV/sixA | putative fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| * | * | ÷ | NC_000913 | 2990599 | 2991475 | 877 | 30 [28] | [28] 32 | [ygeF]–[ygeG] | [ygeF], ygeF, [ygeG] |
| * | * | ÷ | NC_000913 | 3499271 | 3499503 | 233 | 31 [28] | [29] 31 | [yhfL] | [yhfL] |
| * | * | ÷ | NC_000913 | 3769500 | 3770107 | 608 | 33 [29] | [29] 30 | [yibV]–[yibU] | [yibV], yibV, yibU, [yibU] |
| * | * | ÷ | NC_000913 | 3798605 | 3799516 | 912 | 30 [28] | [17] 34 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 3804152 | 3805222 | 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 | 15391 = | NA (NA) | 4 (0.050) | 4/492 | NT | 4.4% | intergenic (+93/‑54) | dnaJ/insL1 | chaperone Hsp40, DnaK co‑chaperone/IS186 transposase |
| ? | NC_000913 | 310053 = | 87 (1.020) | intergenic (‑27/+31) | ecpB/ecpA | ECP production pilus chaperone/ECP pilin | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 84 (0.980) | 61/498 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 825508 | 99 (1.160) | 5 (0.060) | 5/488 | NT | 5.2% | coding (601/1107 nt) | ybhR | putative ABC transporter permease |
| ? | NC_000913 | = 825997 | 84 (1.000) | coding (112/1107 nt) | ybhR | putative ABC transporter permease | |||||
| * | ? | NC_000913 | 1207790 = | 28 (0.330) | 54 (0.670) | 48/466 | NT | 68.3% | 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 (0.620) | 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 | 1293032 = | 0 (0.000) | 88 (1.030) | 56/498 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1387098 | 86 (1.000) | 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 | 91 (1.090) | coding (529/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator, autorepressor, ATPase, phosphatase | |||||
| * | ? | NC_000913 | 1692373 = | 80 (0.930) | 4 (0.050) | 4/496 | NT | 4.8% | coding (479/1266 nt) | uidC | putative outer membrane porin for beta‑glucuronides porin protein |
| ? | NC_000913 | 2101750 = | NA (NA) | intergenic (‑6/+145) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | 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 (0.930) | 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 | 1979486 = | 0 (0.000) | 41 (0.480) | 30/498 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 57 (0.670) | 43/498 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 3567578 | 47 (0.550) | 4 (0.050) | 4/476 | NT | 6.8% | coding (455/1434 nt) | glgA | glycogen synthase |
| ? | NC_000913 | = 3567836 | 64 (0.780) | coding (197/1434 nt) | glgA | glycogen synthase | |||||
| * | ? | NC_000913 | = 3951733 | 6 (0.070) | 80 (0.960) | 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 | 3952060 = | 5 (0.060) | pseudogene (520/663 nt) | ilvG | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted | |||||
| * | ? | NC_000913 | = 4052160 | 80 (0.930) | 4 (0.050) | 3/478 | NT | 4.1% | coding (117/1374 nt) | hemN | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent |
| ? | NC_000913 | = 4052337 | 111 (1.350) | coding (294/1374 nt) | hemN | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent | |||||