mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| RA | 114,992 | G→A | 13.8% | Q245* (CAG→TAG) | hofC ← | assembly protein in type IV pilin biogenesis, transmembrane protein |
| JC JC | 153,986 | IS5 (–) +4 bp | 100% | coding (1438‑1441/2598 nt) | htrE ← | putative outer membrane usher protein |
| RA | 219,501 | C→T | 8.7% | A32T (GCC→ACC) | tsaA ← | tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 418,428 | Δ1 bp | 50.0% | coding (540/1296 nt) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| RA | 701,398 | T→A | 14.5% | D66V (GAT→GTT) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 702,066 | G→C | 54.8% | P229R (CCT→CGT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 906,659 | C→T | 9.0% | R32H (CGC→CAC) | ybjS ← | putative NAD(P)H‑dependent oxidoreductase |
| RA | 1,158,384 | G→A | 100% | W172* (TGG→TGA) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,196,220 | C→T | 41.4% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 41.5% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | 44.5% | L375L (TTA→CTA) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | 48.0% | L375L (TTA→TTG) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,277 | C→T | 27.8% | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,280 | G→C | 27.8% | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,283 | A→G | 29.4% | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| 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 | 1,726,507 | Δ1 bp | 100% | coding (485/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,779,348 | Δ1 bp | 14.8% | intergenic (‑47/‑269) | ydiP ← / → ydiQ | putative DNA‑binding transcriptional regulator/putative electron transfer flavoprotein subunit |
| 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 |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 77.8% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,509,477 | A→C | 18.2% | intergenic (‑51/‑153) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,693,133 | G→A | 7.7% | A804V (GCA→GTA) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,977,595:1 | +C | 100% | coding (997/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| 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 |
| RA | 3,635,801 | Δ1 bp | 8.7% | coding (961/1053 nt) | yhiM → | acid resistance protein, inner membrane |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 3,909,312 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| 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 | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 25.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 15.6% | intergenic (+474/+168) | 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 | 4,451,082 | Δ1 bp | 10.8% | coding (25/1503 nt) | ytfR → | putative sugar ABC transporter ATPase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 720883 | 721166 | 284 | 8 [5] | [5] 6 | [kdpE] | [kdpE] |
| * | * | ÷ | NC_000913 | 1207806 | 1208144 | 339 | 13 [1] | [5] 6 | [stfP]–[tfaP] | [stfP],[tfaP] |
| * | * | ÷ | NC_000913 | 3423936–3424374 | 3424374 | 1–439 | 6 [5] | [5] 6 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4110711 | 4111516 | 806 | 6 [5] | [5] 6 | tpiA | tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 42989 = | 38 (1.130) | 3 (0.090) | 3/478 | NT | 6.9% | coding (587/771 nt) | fixA | anaerobic carnitine reduction putative electron transfer flavoprotein subunit |
| ? | NC_000913 | 43085 = | 44 (1.360) | coding (683/771 nt) | fixA | anaerobic carnitine reduction putative electron transfer flavoprotein subunit | |||||
| * | ? | NC_000913 | 95824 = | 30 (0.890) | 3 (0.090) | 3/478 | NT | 7.9% | coding (1175/1359 nt) | murF | UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase |
| ? | NC_000913 | 96344 = | 41 (1.270) | coding (343/1083 nt) | mraY | phospho‑N‑acetylmuramoyl‑pentapeptide transferase | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 4 (0.120) | 4/498 | NT | 11.4% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 419059 = | 31 (0.920) | coding (1171/1296 nt) | phoR | sensory histidine kinase in two‑component regulatory system with PhoB | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 4 (0.130) | 4/472 | NT | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 606366 | 35 (1.040) | 4 (0.120) | 3/484 | NT | 10.4% | coding (1018/1119 nt) | ybdK | weak gamma‑glutamyl:cysteine ligase |
| ? | NC_000913 | = 606463 | 35 (1.070) | coding (921/1119 nt) | ybdK | weak gamma‑glutamyl:cysteine ligase | |||||
| * | ? | NC_000913 | 759115 = | 59 (1.750) | 4 (0.120) | 4/480 | NT | 7.3% | coding (410/2802 nt) | sucA | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| ? | NC_000913 | 759344 = | 45 (1.380) | coding (639/2802 nt) | sucA | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding | |||||
| * | ? | NC_000913 | = 823202 | 34 (1.010) | 4 (0.120) | 4/486 | NT | 10.4% | coding (538/1242 nt) | clsB | cardiolipin synthase 2 |
| ? | NC_000913 | = 824344 | 36 (1.090) | coding (154/762 nt) | ybhP | endo/exonuclease/phosphatase family protein | |||||
| * | ? | NC_000913 | = 1144833 | 35 (1.040) | 4 (0.120) | 4/486 | NT | 9.5% | intergenic (+11/‑107) | yceQ/rluC | uncharacterized protein/23S rRNA pseudouridine(955,2504,2580) synthase |
| ? | NC_000913 | = 1145097 | 42 (1.280) | coding (158/960 nt) | rluC | 23S rRNA pseudouridine(955,2504,2580) synthase | |||||
| * | ? | NC_000913 | = 1207805 | 1 (0.030) | 8 (0.250) | 7/466 | NT | 89.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 1 (0.030) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2016631 | 35 (1.040) | 4 (0.120) | 3/486 | NT | 13.5% | coding (78/1374 nt) | fliI | flagellum‑specific ATP synthase |
| ? | NC_000913 | = 2017005 | 17 (0.520) | coding (452/1374 nt) | fliI | flagellum‑specific ATP synthase | |||||
| * | ? | NC_000913 | = 2230414 | 40 (1.190) | 3 (0.090) | 3/482 | NT | 7.1% | intergenic (‑29/‑210) | dusC/yohJ | tRNA‑dihydrouridine synthase C/UPF0299 family inner membrane protein |
| ? | NC_000913 | = 2230417 | 40 (1.220) | intergenic (‑32/‑207) | dusC/yohJ | tRNA‑dihydrouridine synthase C/UPF0299 family inner membrane protein | |||||
| * | ? | NC_000913 | 2464885 = | 19 (0.560) | 4 (0.120) | 3/488 | NT | 10.3% | coding (123/756 nt) | mlaA | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| ? | NC_000913 | 2465310 = | 51 (1.540) | coding (10/933 nt) | yfdC | putative inner membrane protein | |||||
| * | ? | NC_000913 | 2791445 = | 41 (1.220) | 4 (0.120) | 4/480 | NT | 10.7% | coding (173/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| ? | NC_000913 | 2791920 = | 27 (0.830) | coding (648/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent | |||||
| * | ? | NC_000913 | = 3150655 | 23 (0.680) | 3 (0.090) | 3/478 | NT | 12.0% | noncoding (102/255 nt) | RIP222 (repetitive extragenic palindromic) element; contains 5 REP sequences and 2 IHF sites | RIP222 (repetitive extragenic palindromic) element; contains 5 REP sequences and 2 IHF sites |
| ? | NC_000913 | = 3150758 | NA (NA) | noncoding (205/255 nt) | RIP222 (repetitive extragenic palindromic) element; contains 5 REP sequences and 2 IHF sites | RIP222 (repetitive extragenic palindromic) element; contains 5 REP sequences and 2 IHF sites | |||||
| * | ? | NC_000913 | = 4327973 | 28 (0.830) | 4 (0.120) | 3/482 | NT | 11.9% | coding (839/2229 nt) | crfC | clamp‑binding sister replication fork colocalization protein, dynamin‑related |
| ? | NC_000913 | = 4328275 | 32 (0.980) | coding (1141/2229 nt) | crfC | clamp‑binding sister replication fork colocalization protein, dynamin‑related | |||||
| * | ? | NC_000913 | = 4553753 | 21 (0.620) | 3 (0.090) | 3/468 | NT | 8.5% | coding (853/1461 nt) | uxuB | D‑mannonate oxidoreductase, NAD‑dependent |
| ? | NC_000913 | = 4554835 | 45 (1.420) | coding (260/774 nt) | uxuR | fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor | |||||
| * | ? | NC_000913 | 4558975 = | 45 (1.330) | 3 (0.090) | 3/480 | NT | 6.6% | coding (552/1173 nt) | iadA | isoaspartyl dipeptidase |
| ? | NC_000913 | 4559021 = | 41 (1.260) | coding (506/1173 nt) | iadA | isoaspartyl dipeptidase | |||||
| * | ? | NC_000913 | 4602975 = | 26 (0.770) | 4 (0.120) | 4/484 | NT | 14.5% | intergenic (‑117/‑502) | yjjP/yjjQ | DUF1212 family inner membrane protein/putative transcriptional regulator |
| ? | NC_000913 | 4603100 = | 22 (0.670) | intergenic (‑242/‑377) | yjjP/yjjQ | DUF1212 family inner membrane protein/putative transcriptional regulator | |||||