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] | |
| RA | 526,792 | A→C | 8.2% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 7.8% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 1,097,158 | C→T | 12.9% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,196,220 | C→T | 17.4% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 16.5% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | 15.1% | L375L (TTA→CTA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | 15.4% | L375L (TTA→TTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,277 | C→T | 12.6% | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,280 | G→C | 12.5% | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,283 | A→G | 12.2% | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,292 | C→T | 9.7% | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,304 | G→A | 11.3% | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,316 | T→A | 9.6% | D398E (GAT→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,325 | A→G | 9.3% | K401K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,313,750 | Δ1 bp | 8.5% | intergenic (‑87/‑270) | yciC ← / → ompW | UPF0259 family inner membrane protein/outer membrane protein W |
| RA | 1,529,175 | T→C | 24.8% | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | 24.4% | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | 24.0% | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | 27.0% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,621,022 | C→A | 6.4% | R39L (CGC→CTC) | eamA ← | cysteine and O‑acetyl‑L‑serine efflux system |
| RA | 1,708,718 | G→A | 5.9% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,805 | T→C | 9.7% | R629R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| JC JC | 1,907,242 | IS5 (+) +4 bp | 43.3% | coding (191‑194/210 nt) | cspC ← | stress protein, member of the CspA‑family |
| JC JC | 1,907,562 | IS1 (+) +9 bp | 45.1% | coding (22‑30/144 nt) | yobF ← | DUF2527 family heat‑induced protein |
| 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 | 2,304,523 | G→C | 8.9% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,798 | T→C | 12.1% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,988 | T→C | 5.8% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,013 | A→G | 6.8% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC | 2,765,412 | Δ8 bp | 5.7% | intergenic (‑259/+94) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,800,671 | A→G | 5.2% | intergenic (+196/‑52) | ygaM → / → nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| RA | 2,967,417 | G→A | 51.2% | Q340* (CAG→TAG) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| JC | 3,130,012 | Δ3 bp | 2.1% | pseudogene (130‑132/1101 nt) | yghO ← | pseudogene, IS‑interrupted |
| JC | 3,152,792 | Δ3 bp | 2.5% | coding (557‑559/1188 nt) | metC → | cystathionine beta‑lyase, PLP‑dependent |
| RA | 3,442,896 | A→T | 54.7% | F401Y (TTC→TAC) | secY ← | preprotein translocase membrane subunit |
| 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 | 3,815,801 | Δ1 bp | 100% | intergenic (‑33/+33) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 39.5% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,183,116 | +45 bp | 2.1% | coding (1872/4029 nt) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,184,800 | G→A | 32.7% | V1186M (GTG→ATG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,187,507 | A→C | 56.2% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,187,633 | A→C | 6.0% | N762H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,190 | A→G | 11.2% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 12.5% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 36.6% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 21.6% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 16.2% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 16.8% | 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 | 4,325,948 | A→G | 5.8% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,088 | T→G | 9.2% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,496,014 | T→C | 6.8% | I66V (ATT→GTT) | ahr ← | broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 720726 | 721166 | 441 | 56 [55] | [54] 56 | [ybfK]–[kdpE] | [ybfK], [kdpE] |
| * | * | ÷ | NC_000913 | 1063837 | 1064545 | 709 | 56 [49] | [55] 56 | [yccE] | [yccE] |
| * | * | ÷ | NC_000913 | 1196442 | 1198724 | 2283 | 56 [55] | [53] 58 | ymfD–[lit] | ymfD, ymfE, [lit] |
| * | * | ÷ | NC_000913 | 1210984 | 1212881 | 1898 | 56 [54] | [53] 62 | [mcrA]–[ycgX] | [mcrA], icdC, iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1299278 | 1301021 | 1744 | 57 [53] | [55] 59 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1529849 | 1530579 | 731 | 56 [55] | [55] 56 | [rhsE]–ydcD | [rhsE], ydcD |
| * | * | ÷ | NC_000913 | 1978342 | 1979748 | 1407 | 61 [55] | [54] 58 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2033368 | 2034172 | 805 | 56 [54] | [54] 56 | [yedR]–[yedS] | [yedR], [yedS] |
| * | * | ÷ | NC_000913 | 2105130 | 2107460 | 2331 | 56 [54] | [51] 57 | [wbbI]–[glf] | [wbbI], wbbH, [glf] |
| * | * | ÷ | NC_000913 | 2468994 | 2469904 | 911 | 56 [54] | [54] 56 | [gtrB]–[gtrS] | [gtrB], [gtrS] |
| * | * | ÷ | NC_000913 | 2469929 | 2470736 | 808 | 56 [54] | [54] 56 | [gtrS] | [gtrS] |
| * | * | ÷ | NC_000913 | 2784392 | 2785601 | 1210 | 58 [54] | [52] 56 | [ypjC] | [ypjC] |
| * | * | ÷ | NC_000913 | 2990612 | 2991397 | 786 | 56 [50] | [53] 57 | [ygeF]–[ygeG] | [ygeF], ygeF, [ygeG] |
| * | * | ÷ | NC_000913 | 3423829–3424471 | 3424471 | 1–643 | 61 [55] | [55] 56 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3581630 | 3582299 | 670 | 56 [48] | [52] 56 | [yhhZ] | [yhhZ] |
| * | * | ÷ | NC_000913 | 3796873 | 3800570 | 3698 | 57 [54] | [52] 56 | [waaC]–[waaY] | [waaC], waaL, waaU, waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 3804080 | 3805239 | 1160 | 56 [54] | [53] 56 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4078448 | 4079586 | 1139 | 56 [55] | [54] 57 | yiiE | yiiE |
| * | * | ÷ | NC_000913 | 4571623 | 4572640 | 1018 | 62 [50] | [55] 57 | yjiS–[yjiT] | yjiS, [yjiT] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 61 (0.530) | 51 (0.470) | 42/518 | NT | 48.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 50 (0.460) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 60 (0.520) | 78 (0.720) | 57/518 | NT | 59.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 50 (0.460) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 18 (0.160) | 17/542 | 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) | 17 (0.150) | 17/534 | 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 | = 2957101 | 121 (1.050) | 3 (0.030) | 3/534 | NT | 2.4% | coding (1784/2889 nt) | ptrA | protease III |
| ? | NC_000913 | = 2957112 | 122 (1.090) | coding (1773/2889 nt) | ptrA | protease III | |||||
| * | ? | NC_000913 | = 3814427 | 119 (1.030) | 4 (0.040) | 4/534 | NT | 3.3% | intergenic (+40/‑67) | dut/slmA | deoxyuridinetriphosphatase/nucleoid occlusion factor, anti‑FtsZ division inhibitor |
| ? | NC_000913 | = 3814432 | 120 (1.070) | intergenic (+45/‑62) | dut/slmA | deoxyuridinetriphosphatase/nucleoid occlusion factor, anti‑FtsZ division inhibitor | |||||
| * | ? | NC_000913 | = 3894310 | 120 (1.040) | 3 (0.030) | 3/534 | NT | 2.5% | coding (430/750 nt) | yieE | phosphopantetheinyl transferase superfamily protein |
| ? | NC_000913 | = 3894317 | 114 (1.020) | coding (437/750 nt) | yieE | phosphopantetheinyl transferase superfamily protein | |||||