mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
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 | 1,104,717 | Δ4 bp | 2.3% | coding (271‑274/456 nt) | csgA → | curlin subunit, amyloid curli fibers, cryptic |
| RA | 1,286,965 | A→G | 12.0% | intergenic (+439/+122) | narI → / ← tpr | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein |
| RA | 1,355,035 | G→A | 37.5% | R146C (CGT→TGT) | sapB ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,466,604 | G→A | 7.3% | pseudogene (1213/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| JC JC | 1,907,448 | IS5 (–) +4 bp | 100% | coding (141‑144/144 nt) | yobF ← | DUF2527 family heat‑induced protein |
| RA | 2,173,360 | Δ1 bp | 6.4% | pseudogene (3/442 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 | 2,173,361 | 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 | 2,304,798 | T→C | 7.0% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,966,573 | T→G | 5.8% | D621A (GAT→GCT) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| JC | 2,966,777 | Δ4 bp | 1.8% | coding (1655‑1658/2247 nt) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| JC | 2,967,354 | Δ189 bp | 3.4% | coding (893‑1081/2247 nt) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,560,455 | +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 |
| JC | 3,736,653 | Δ3 bp | 2.6% | coding (523‑525/825 nt) | bax ← | putative glucosaminidase |
| RA | 3,802,236 | C→A | 37.8% | D275Y (GAT→TAT) | waaO ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase |
| RA | 3,815,809 | Δ1 bp | 41.8% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,815,810 | G→T | 48.6% | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 2.2% | [rph]–[rph] | [rph], [rph] | |
| JC | 3,816,605 | Δ103 bp | 9.0% | [yicC] | [yicC] | |
| RA | 3,966,721 | G→T | 26.9% | R102L (CGC→CTC) | rho → | transcription termination factor |
| RA | 4,187,507 | A→C | 100% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,190 | A→G | 18.1% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 19.7% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 35.6% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 27.1% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 11.8% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 11.9% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +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 | 83906 | 84365 | 460 | 51 [46] | [48] 49 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | NC_000913 | 384625 | 385182 | 558 | 51 [42] | [48] 50 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 582654 | 584736 | 2083 | 49 [47] | [48] 49 | [ybcY]–[ompT] | [ybcY], ybcY, tfaX, appY, [ompT] |
| * | * | ÷ | NC_000913 | 733583 | 734311 | 729 | 49 [48] | [48] 49 | [rhsC]–[rhsO] | [rhsC], ybfB, [rhsO] |
| * | * | ÷ | NC_000913 | 954489 | 954850 | 362 | 49 [46] | [48] 49 | focA/ycaO | formate channel/ribosomal protein S12 methylthiotransferase accessory factor |
| * | * | ÷ | NC_000913 | 1196546 | 1198708 | 2163 | 50 [46] | [48] 49 | ymfD–[lit] | ymfD, ymfE, [lit] |
| * | * | ÷ | NC_000913 | 1812466 | 1813458 | 993 | 50 [48] | [48] 50 | [ydjO]–[cedA] | [ydjO], [cedA] |
| * | * | ÷ | NC_000913 | 1978205 | 1979738 | 1534 | 49 [48] | [46] 50 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2103172 | 2104364 | 1193 | 49 [48] | [48] 51 | [wbbL]–[wbbK] | [wbbL], [wbbK] |
| * | * | ÷ | NC_000913 | 2192041 | 2192665 | 625 | 51 [48] | [48] 52 | [yehD]–[yehE] | [yehD], [yehE] |
| * | * | ÷ | NC_000913 | 2469011 | 2470791 | 1781 | 49 [48] | [48] 49 | [gtrB]–gtrS | [gtrB], gtrS |
| * | * | ÷ | NC_000913 | 2590892 | 2591311 | 420 | 50 [48] | [48] 53 | [yffB] | [yffB] |
| * | * | ÷ | NC_000913 | 2773231 | 2774116 | 886 | 52 [47] | [47] 49 | [yfjW] | [yfjW] |
| * | * | ÷ | NC_000913 | 2785807 | 2786990 | 1184 | 50 [48] | [48] 50 | [ileY]–[ygaQ] | [ileY], [ygaQ] |
| * | * | ÷ | NC_000913 | 2884142 | 2884532 | 391 | 49 [47] | [48] 50 | casA/ygcB | CRISP RNA (crRNA) containing Cascade antiviral complex protein/Cascade complex anti‑viral R‑loop helicase‑annealase Cas3 |
| * | * | ÷ | NC_000913 | 2988205 | 2988526 | 322 | 50 [45] | [48] 50 | [yqeI] | [yqeI] |
| * | * | ÷ | NC_000913 | 2990578 | 2993004 | 2427 | 51 [48] | [48] 50 | [ygeF]–[ygeH] | [ygeF], ygeF, ygeG, [ygeH] |
| * | * | ÷ | NC_000913 | 2994652 | 2996114 | 1463 | 49 [47] | [48] 50 | [ygeK]–[ygeO] | [ygeK], ygeN, ygeN, [ygeO] |
| * | * | ÷ | NC_000913 | 3267922 | 3269738 | 1817 | 54 [45] | [47] 52 | [yhaB]–yhaC | [yhaB], yhaC |
| * | * | ÷ | NC_000913 | 3423875–3424493 | 3424493 | 1–619 | 49 [48] | [48] 49 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3581630 | 3584873 | 3244 | 49 [41] | [48] 49 | yhhZ–[yrhB] | yhhZ, yrhA, insA, insB1, yrhA, [yrhB] |
| * | * | ÷ | NC_000913 | 3769333 | 3770359 | 1027 | 50 [48] | [47] 49 | yibV–[yibH] | yibV, yibV, yibU, yibU, [yibH] |
| * | * | ÷ | NC_000913 | 3796873 | 3800409 | 3537 | 50 [48] | [48] 50 | [waaC]–[waaY] | [waaC], waaL, waaU, waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 3800675 | 3801413 | 739 | 50 [46] | [48] 50 | [waaY]–[waaR] | [waaY], [waaR] |
| * | * | ÷ | NC_000913 | 3804046 | 3805242 | 1197 | 49 [47] | [44] 49 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4282099 | 4283338 | 1240 | 52 [47] | [47] 49 | [yjcF]–[actP] | [yjcF], [actP] |
| * | * | ÷ | NC_000913 | 4475662 | 4477281 | 1620 | 50 [48] | [48] 49 | [yjgL] | [yjgL] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1096961 = | 80 (0.720) | 10 (0.130) | 6/388 | NT | 14.5% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 61 (0.780) | intergenic (+674/+62) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 63 (0.570) | 39 (0.370) | 34/516 | NT | 43.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 43 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 58 (0.520) | 40 (0.380) | 34/516 | NT | 45.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 43 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 12 (0.110) | 12/540 | 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) | 6 (0.060) | 6/532 | 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 | = 2565939 | 113 (1.020) | 3 (0.030) | 3/532 | NT | 2.6% | coding (946/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase |
| ? | NC_000913 | = 2565954 | 112 (1.040) | coding (931/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | NC_000913 | = 3229785 | 147 (1.320) | 3 (0.030) | 3/534 | NT | 2.0% | coding (898/2352 nt) | ygjK | alpha‑glucosidase |
| ? | NC_000913 | = 3229797 | 150 (1.390) | coding (910/2352 nt) | ygjK | alpha‑glucosidase | |||||