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 | 21.4% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 19.7% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 1,097,158 | C→T | 11.4% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,287,360 | A→T | 8.5% | intergenic (‑32/+178) | tyrV ← / ← tyrT | tRNA‑Tyr/tRNA‑Tyr |
| RA | 1,466,138 | G→A | 5.0% | pseudogene (747/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,201 | T→C | 11.8% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 7.3% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 6.6% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,270 | C→T | 7.0% | pseudogene (879/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,438 | T→G | 7.6% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,579 | G→C | 9.6% | pseudogene (1188/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,604 | G→A | 8.0% | pseudogene (1213/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,618 | T→C | 6.8% | pseudogene (1227/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,636 | T→C | 5.8% | pseudogene (1245/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,711 | T→C | 9.0% | pseudogene (1320/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,529,175 | T→C | 100% | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | 100% | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | 94.9% | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | 100% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,708,724 | G→A | 7.2% | K602K (AAG→AAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 5.6% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,847 | G→A | 8.1% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,756,457 | +A | 86.2% | coding (760/1413 nt) | pykF → | pyruvate kinase I |
| JC JC | 1,907,562 | IS1 (+) +9 bp | 100% | coding (22‑30/144 nt) | yobF ← | DUF2527 family heat‑induced protein |
| RA | 1,915,288 | G→C | 11.8% | L83V (CTT→GTT) | proQ ← | RNA chaperone, putative ProP translation regulator |
| 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 | 2,966,582 | C→T | 83.6% | G618D (GGC→GAC) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,440,065 | G→A | 6.8% | P322L (CCA→CTA) | rpoA ← | RNA polymerase, alpha 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 |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,529 | C→G | 14.5% | S31C (TCC→TGC) | yidX → | putative lipoprotein |
| RA | 4,296,190 | A→G | 17.7% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 18.3% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 33.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 22.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 8.0% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 13.5% | 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 | 1978311 | 1979738 | 1428 | 67 [66] | [66] 69 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2033458 | 2034167 | 710 | 70 [64] | [64] 68 | [yedR]–[yedS] | [yedR], [yedS] |
| * | * | ÷ | NC_000913 | 2469055 | 2470731 | 1677 | 67 [65] | [63] 71 | [gtrB]–gtrS | [gtrB], gtrS |
| * | * | ÷ | NC_000913 | 3769369 | 3770269 | 901 | 67 [65] | [66] 67 | [yibV]–[yibH] | [yibV], yibV, yibU, yibU, [yibH] |
| * | * | ÷ | NC_000913 | 3796854 | 3800422 | 3569 | 67 [66] | [66] 67 | [waaC]–[waaY] | [waaC], waaL, waaU, waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 4476442 | 4477245 | 804 | 67 [66] | [57] 68 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 6300 = | 141 (1.060) | 3 (0.020) | 3/514 | NT | 2.2% | coding (160/777 nt) | yaaA | peroxide resistance protein, lowers intracellular iron |
| ? | NC_000913 | 6318 = | 130 (1.050) | coding (142/777 nt) | yaaA | peroxide resistance protein, lowers intracellular iron | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 4 (0.030) | 4/550 | NT | 2.3% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1771038 = | 173 (1.310) | intergenic (+67/‑33) | ydiL/ydiM | putative HTH domain DNA‑binding protein/putative MFS transporter, membrane protein | |||||
| * | ? | NC_000913 | 285874 = | 119 (0.900) | 3 (0.020) | 3/534 | NT | 2.5% | coding (480/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter |
| ? | NC_000913 | 285896 = | 117 (0.910) | coding (502/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter | |||||
| * | ? | NC_000913 | 324960 = | 138 (1.040) | 4 (0.030) | 4/550 | NT | 2.8% | coding (405/669 nt) | ykgH | putative inner membrane protein |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 78 (0.590) | 61 (0.490) | 45/518 | NT | 45.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 74 (0.590) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 76 (0.570) | 73 (0.580) | 57/518 | NT | 50.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 74 (0.590) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 30 (0.230) | 22/542 | 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 | = 1651548 | NA (NA) | 4 (0.030) | 4/550 | NT | 2.4% | noncoding (706/706 nt) | IS2 | repeat region |
| ? | NC_000913 | 1755828 = | 162 (1.220) | coding (131/1413 nt) | pykF | pyruvate kinase I | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 34 (0.260) | 28/534 | 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 | 2288919 = | NA (NA) | 10 (0.080) | 6/550 | NT | 6.0% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2365124 | 158 (1.190) | coding (497/603 nt) | ais | putative LPS core heptose(II)‑phosphate phosphatase | |||||
| * | ? | NC_000913 | = 2515616 | NA (NA) | 3 (0.020) | 3/544 | NT | 2.3% | noncoding (1344/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 4543608 = | 129 (0.980) | coding (494/549 nt) | fimA | major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 2882234 = | 132 (1.000) | 3 (0.020) | 3/514 | NT | 2.4% | coding (404/483 nt) | casB | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| ? | NC_000913 | 2882252 = | 122 (0.990) | coding (386/483 nt) | casB | CRISP RNA (crRNA) containing Cascade antiviral complex protein | |||||