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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| JC | 417,075 | (TCATAAATCTG)2→1 | 27.6% | intergenic (‑123/‑57) | sbcD ← / → phoB | exonuclease, dsDNA, ATP‑dependent/response regulator in two‑component regulatory system with PhoR |
| RA | 702,000 | T→G | 5.2% | H251P (CAT→CCT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,306 | C→T | 27.5% | R149H (CGT→CAT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,330 | Δ1 bp | 34.0% | coding (422/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,390 | T→G | 17.9% | H121P (CAT→CCT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| JC | 1,159,282 | +AGT | 100% | coding (1414/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| 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 |
| RA | 1,726,004 | G→A | 100% | intergenic (‑84/‑19) | ydhL ← / → nemR | DUF1289 family protein/transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,756,980 | Δ1 bp | 11.9% | coding (1283/1413 nt) | pykF → | pyruvate kinase I |
| 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 | 2,352,561 | G→T | 11.2% | intergenic (‑187/‑86) | glpT ← / → glpA | sn‑glycerol‑3‑phosphate transporter/anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| JC JC | 2,374,949 | IS186 (+) +7 bp :: Δ3 bp | 16.6% | coding (49‑55/1356 nt) | menE ← | O‑succinylbenzoate‑CoA ligase |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 53.0% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,976,909 | A→C | 100% | E104A (GAG→GCG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,455,874 | A→G | 6.7% | T99T (ACA→ACG) | gspC → | general secretory pathway component, cryptic |
| RA | 3,512,275 | T→C | 5.8% | K24E (AAG→GAG) | yhfZ ← | putative DNA‑binding transcriptional regulator |
| 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] | |
| RA | 3,875,522 | C→G | 21.6% | L29V (CTG→GTG) | yidX → | putative lipoprotein |
| RA | 3,875,525 | G→T | 15.6% | V30F (GTT→TTT) | yidX → | putative lipoprotein |
| MC JC | 3,909,312 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| JC JC | 3,922,629 | IS5 (–) +4 bp | 28.3% | intergenic (‑189/+425) | atpI ← / ← rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein |
| RA | 3,966,736 | G→A | 10.9% | G107D (GGT→GAT) | rho → | transcription termination factor |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,171,648 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,178,223 | T→C | 8.8% | S161P (TCT→CCT) | nusG → | transcription termination factor |
| RA | 4,181,851 | A→C | 11.5% | K203Q (AAA→CAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 13.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 20.5% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 24.1% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 26.5% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 15.1% | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978444 | 1979397 | 954 | 45 [44] | [41] 46 | insB1–insA | insB1,insA |
| * | * | ÷ | NC_000913 | 3798525 | 3799765 | 1241 | 45 [43] | [38] 45 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 3804155 | 3805248 | 1094 | 45 [43] | [44] 49 | waaS–[waaP] | waaS,[waaP] |
| * | * | ÷ | NC_000913 | 4110655 | 4111575 | 921 | 45 [42] | [44] 45 | [cdh]–tpiA | [cdh],tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 258675 | NA (NA) | 10 (0.090) | 10/520 | NT | 8.4% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 465152 = | 109 (1.000) | coding (396/696 nt) | queC | 7‑cyano‑7‑deazaguanine (preQ0) synthase; queuosine biosynthesis | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 3 (0.030) | 3/496 | NT | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 41 (0.370) | 44 (0.430) | 37/490 | NT | 49.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 52 (0.500) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 39 (0.360) | 80 (0.780) | 55/490 | NT | 64.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 52 (0.500) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 67 (0.620) | 55/514 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 21 (0.200) | 17/506 | 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 | 3467131 = | 50 (0.460) | 4 (0.040) | 4/506 | NT | 7.7% | intergenic (‑140/+29) | bfd/chiA | bacterioferritin‑associated ferredoxin/periplasmic endochitinase |
| ? | NC_000913 | 3467153 = | 48 (0.450) | intergenic (‑162/+7) | bfd/chiA | bacterioferritin‑associated ferredoxin/periplasmic endochitinase | |||||