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 JC | 573,890 | IS5 (–) +4 bp | 92.5% | intergenic (+20/‑63) | ylcG → / → quuD | uncharacterized protein, DLP12 prophage/DLP12 prophage; putative antitermination protein |
| RA | 657,541 | G→T | 100% | intergenic (+40/+14) | cspE → / ← flc | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein |
| JC | 795,265 | Δ3 bp | 3.4% | coding (177‑179/774 nt) | modA → | molybdate ABC transporter periplasmic binding protein; chlorate resistance protein |
| RA | 914,845 | G→A | 6.4% | L5L (CTG→TTG) | ybjE ← | putative transporter |
| RA | 1,466,604 | G→A | 10.7% | pseudogene (1213/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,711 | T→C | 6.6% | pseudogene (1320/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,713 | C→A | 6.4% | pseudogene (1322/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,714 | T→C | 6.0% | pseudogene (1323/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,717 | C→T | 8.0% | pseudogene (1326/2513 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 |
| RA | 1,708,718 | G→A | 8.7% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,748 | G→C | 5.2% | A610A (GCG→GCC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,751 | A→G | 7.9% | E611E (GAA→GAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 9.0% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 5.9% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| 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 | 2,187,596 | T→C | 7.8% | G273G (GGA→GGG) | yehA ← | putative fimbrial‑like adhesin protein |
| RA | 2,304,798 | T→C | 10.8% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,905,987 | G→A | 5.4% | G93R (GGG→AGG) | ygcG → | TPM domain protein, putative phosphatase |
| RA | 2,911,534 | Δ1 bp | 87.5% | coding (2118/2235 nt) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| JC | 3,400,539 | Δ3 bp | 2.1% | coding (547‑549/1044 nt) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| 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 |
| RA | 3,888,180 | T→A | 6.1% | C451* (TGT→TGA) | mnmE → | tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase |
| RA | 4,187,507 | A→C | 100% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,190 | A→G | 22.3% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 26.0% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 30.0% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 19.9% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 12.4% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 11.7% | 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 |
| RA | 4,326,088 | T→G | 7.1% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,494,473 | A→G | 7.0% | intergenic (‑67/‑150) | idnD ← / → idnK | L‑idonate 5‑dehydrogenase, NAD‑binding/D‑gluconate kinase, thermosensitive |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 238038 | 238888 | 851 | 48 [47] | [46] 50 | [yafT]–[yafU] | [yafT], ykfM, [yafU] |
| * | * | ÷ | NC_000913 | 384535 | 385181 | 647 | 50 [45] | [47] 48 | [yaiS] | [yaiS] |
| * | * | ÷ | NC_000913 | 389771 | 390240 | 470 | 48 [43] | [47] 49 | hemB/yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| * | * | ÷ | NC_000913 | 582651 | 584758 | 2108 | 48 [47] | [45] 50 | [ybcY]–[ompT] | [ybcY], ybcY, tfaX, appY, [ompT] |
| * | * | ÷ | NC_000913 | 997428 | 998063 | 636 | 48 [47] | [46] 53 | [ssuE]–[elfA] | [ssuE], [elfA] |
| * | * | ÷ | NC_000913 | 1092334 | 1093163 | 830 | 48 [46] | [47] 48 | [ycdT] | [ycdT] |
| * | * | ÷ | NC_000913 | 1210978 | 1212937 | 1960 | 48 [47] | [44] 49 | [mcrA]–[ycgX] | [mcrA], icdC, iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1216032 | 1216814 | 783 | 48 [47] | [47] 48 | ymgA–[ymgC] | ymgA, ariR, [ymgC] |
| * | * | ÷ | NC_000913 | 1526731 | 1527819 | 1089 | 50 [47] | [47] 48 | [yncG]–yncH | [yncG], yncH |
| * | * | ÷ | NC_000913 | 1529881 | 1530589 | 709 | 48 [45] | [42] 48 | [rhsE]–[yncI] | [rhsE], ydcD, [yncI] |
| * | * | ÷ | NC_000913 | 1582373 | 1582938 | 566 | 52 [47] | [47] 49 | [ydeN]–[ydeO] | [ydeN], [ydeO] |
| * | * | ÷ | NC_000913 | 1812565 | 1813392 | 828 | 48 [47] | [47] 48 | [ydjO] | [ydjO] |
| * | * | ÷ | NC_000913 | 1978342 | 1979720 | 1379 | 48 [47] | [47] 48 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2103219 | 2104458 | 1240 | 48 [46] | [47] 48 | [wbbL]–[wbbK] | [wbbL], [wbbK] |
| * | * | ÷ | NC_000913 | 2469007 | 2470801 | 1795 | 48 [44] | [47] 49 | [gtrB]–gtrS | [gtrB], gtrS |
| * | * | ÷ | NC_000913 | 2590895 | 2591402 | 508 | 49 [47] | [47] 48 | [yffB] | [yffB] |
| * | * | ÷ | NC_000913 | 2774200 | 2775569 | 1370 | 48 [47] | [46] 49 | [yfjW]–[ypjI] | [yfjW], [ypjI] |
| * | * | ÷ | NC_000913 | 2785739 | 2787064 | 1326 | 48 [44] | [47] 48 | ileY–[ygaQ] | ileY, [ygaQ] |
| * | * | ÷ | NC_000913 | 2990524 | 2993127 | 2604 | 49 [47] | [47] 49 | ygeF–[ygeH] | ygeF, ygeF, ygeG, [ygeH] |
| * | * | ÷ | NC_000913 | 2994623 | 2996131 | 1509 | 50 [46] | [37] 49 | [ygeK]–[ygeO] | [ygeK], ygeN, ygeN, [ygeO] |
| * | * | ÷ | NC_000913 | 3136347 | 3136685 | 339 | 50 [46] | [43] 51 | [pitB]–[gss] | [pitB], [gss] |
| * | * | ÷ | NC_000913 | 3185143 | 3185517 | 375 | 49 [46] | [45] 48 | [ygiL] | [ygiL] |
| * | * | ÷ | NC_000913 | 3267785 | 3269780 | 1996 | 51 [47] | [47] 48 | yhaB–yhaC | yhaB, yhaC |
| * | * | ÷ | NC_000913 | 3360714 | 3361349 | 636 | 48 [46] | [45] 52 | [gltF] | [gltF] |
| * | * | ÷ | NC_000913 | 3423839–3424234 | 3424482–3424238 | 5–644 | 50 [47] | [46] 53 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3469776 | 3470554–3470164 | 389–779 | 48 [47] | [47] 50 | [chiA]–[tufA] | [chiA], [tufA] |
| * | * | ÷ | NC_000913 | 3581611 | 3584929 | 3319 | 63 [46] | [45] 49 | [yhhY]–[yrhB] | [yhhY], yhhZ, yrhA, insA, insB1, yrhA, [yrhB] |
| * | * | ÷ | NC_000913 | 3623146 | 3624459 | 1314 | 49 [47] | [47] 50 | [rhsB]–[yhhI] | [rhsB], yhhH, yrhC, [yhhI] |
| * | * | ÷ | NC_000913 | 3631637 | 3634993 | 3357 | 48 [47] | [45] 49 | [yhiJ]–[yhiM] | [yhiJ], yhiL, yhiL, [yhiM] |
| * | * | ÷ | NC_000913 | 3652170–3653236 | 3654019 | 784–1850 | 51 [47] | [47] 48 | insH1–[slp] | insH1, yhiS, [slp] |
| * | * | ÷ | NC_000913 | 3751723 | 3752392 | 670 | 49 [45] | [47] 48 | [yiaT]–[yiaU] | [yiaT], [yiaU] |
| * | * | ÷ | NC_000913 | 3757778 | 3758118 | 341 | 49 [46] | [44] 50 | [yiaY]–[selB] | [yiaY], [selB] |
| * | * | ÷ | NC_000913 | 3767707 | 3770279 | 2573 | 48 [47] | [46] 49 | [rhsJ]–[yibH] | [rhsJ], yibG, yibS, yibW, yibW, yibV, yibV, yibU, yibU, [yibH] |
| * | * | ÷ | NC_000913 | 3796872 | 3800382 | 3511 | 48 [41] | [46] 48 | [waaC]–[waaY] | [waaC], waaL, waaU, waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 3800657 | 3802486 | 1830 | 48 [47] | [41] 48 | [waaY]–[waaO] | [waaY], waaR, [waaO] |
| * | * | ÷ | NC_000913 | 3803980 | 3805278 | 1299 | 48 [46] | [45] 48 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4043836 | 4044319 | 484 | 48 [47] | [47] 48 | [dsbA]–[yihF] | [dsbA], [yihF] |
| * | * | ÷ | NC_000913 | 4221509 | 4222730 | 1222 | 50 [47] | [46] 48 | [arpA] | [arpA] |
| * | * | ÷ | NC_000913 | 4250622 | 4251219 | 598 | 48 [47] | [47] 49 | yjbI–[yjbI] | yjbI, yjbI, [yjbI] |
| * | * | ÷ | NC_000913 | 4268371 | 4269395 | 1025 | 48 [46] | [47] 49 | yjbS | yjbS |
| * | * | ÷ | NC_000913 | 4312955 | 4313256 | 302 | 48 [32] | [46] 48 | [alsR] | [alsR] |
| * | * | ÷ | NC_000913 | 4476390 | 4477209 | 820 | 48 [47] | [47] 48 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| * | * | ÷ | NC_000913 | 4479389 | 4479888 | 500 | 49 [47] | [46] 48 | [yjgM]–[yjgN] | [yjgM], [yjgN] |
| * | * | ÷ | NC_000913 | 4541528 | 4542038 | 511 | 48 [46] | [45] 49 | [fimB]–[fimE] | [fimB], [fimE] |
| * | * | ÷ | NC_000913 | 4602919 | 4603656 | 738 | 49 [43] | [47] 49 | [yjjQ] | [yjjQ] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 208127 = | 119 (1.080) | 4 (0.040) | 4/526 | NT | 3.2% | coding (3002/3483 nt) | dnaE | DNA polymerase III alpha subunit |
| ? | NC_000913 | 208161 = | 124 (1.170) | coding (3036/3483 nt) | dnaE | DNA polymerase III alpha subunit | |||||
| * | ? | NC_000913 | 503443 = | 38 (0.350) | 3 (0.030) | 3/522 | NT | 7.6% | intergenic (‑205/+33) | ybaL/fsr | inner membrane putative NAD(P)‑binding transporter/putative fosmidomycin efflux system protein |
| ? | NC_000913 | 503470 = | 37 (0.350) | intergenic (‑232/+6) | ybaL/fsr | inner membrane putative NAD(P)‑binding transporter/putative fosmidomycin efflux system protein | |||||
| * | ? | NC_000913 | 1096961 = | 73 (0.660) | 17 (0.220) | 3/384 | NT | 22.4% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 66 (0.850) | intergenic (+674/+62) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 48 (0.440) | 41 (0.400) | 37/512 | NT | 49.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 39 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 44 (0.400) | 45 (0.430) | 38/512 | NT | 52.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 39 (0.380) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 8 (0.070) | 8/536 | 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 | 1393771 = | 139 (1.260) | 5 (0.050) | 5/544 | NT | 3.5% | coding (545/1614 nt) | mppA | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1879829 = | 78 (0.710) | 6 (0.050) | 5/540 | NT | 7.1% | coding (120/360 nt) | yeaR | DUF1971 family protein, nitrate‑inducible |
| ? | NC_000913 | = 2515616 | NA (NA) | noncoding (1344/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 9 (0.080) | 9/528 | 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 | = 3154353 | 121 (1.100) | 3 (0.030) | 3/526 | NT | 2.5% | coding (866/957 nt) | yqhC | transcriptional activator of yqhD |
| ? | NC_000913 | = 3154366 | 121 (1.140) | coding (853/957 nt) | yqhC | transcriptional activator of yqhD | |||||
| * | ? | NC_000913 | 3976392 = | 124 (1.130) | 5 (0.050) | 5/530 | NT | 4.0% | coding (115/1251 nt) | wzxE | O‑antigen translocase |
| ? | NC_000913 | 3976413 = | 118 (1.100) | coding (136/1251 nt) | wzxE | O‑antigen translocase | |||||