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 | 20.9% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 20.3% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 1,352,926 | C→A | 16.1% | G235C (GGT→TGT) | sapD ← | antimicrobial peptide ABC transporter ATPase |
| RA | 1,357,070 | A→C | 85.0% | L14R (CTT→CGT) | sapA ← | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| RA | 1,466,418 | A→G | 7.0% | pseudogene (1027/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,435 | A→G | 7.8% | pseudogene (1044/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,438 | T→G | 6.3% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,713 | C→A | 7.0% | pseudogene (1322/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,714 | T→C | 6.1% | pseudogene (1323/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,726 | G→A | 8.0% | pseudogene (1335/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 5.9% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,856 | A→G | 5.6% | pseudogene (1465/2513 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 | 100% | 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 |
| JC JC | 1,907,448 | IS5 (+) +4 bp | 100% | coding (141‑144/144 nt) | yobF ← | DUF2527 family heat‑induced protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 8.1% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,373,105 | G→T | 7.1% | A72S (GCG→TCG) | arnF → | undecaprenyl phosphate‑alpha‑L‑ara4N exporter; flippase ArnEF subunit |
| RA | 2,918,684 | G→A | 5.3% | L234L (CTC→CTT) | gudD ← | D‑glucarate dehydratase 1 |
| RA | 2,994,054 | A→T | 6.8% | pseudogene (116/444 nt) | pbl → | pseudogene, peptidoglycan‑binding enzyme family |
| JC | 3,383,196 | Δ3 bp | 2.6% | coding (997‑999/1068 nt) | degS → | serine endoprotease, periplasmic |
| 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 |
| RA | 4,185,642 | G→A | 94.6% | R98H (CGC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,186,542 | A→T | 7.0% | K398M (AAG→ATG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,190 | A→G | 16.2% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 16.6% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 26.5% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 21.3% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 9.0% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 8.7% | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3769507 | 3770108 | 602 | 52 [48] | [48] 49 | [yibV]–[yibU] | [yibV], yibV, yibU, [yibU] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 49 (0.420) | 41 (0.370) | 37/514 | NT | 44.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 57 (0.520) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 48 (0.410) | 29 (0.270) | 24/514 | NT | 36.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 57 (0.520) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 40 (0.350) | 35/538 | 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 | = 1879834 | 95 (0.830) | 3 (0.030) | 3/540 | NT | 3.1% | coding (115/360 nt) | yeaR | DUF1971 family protein, nitrate‑inducible |
| ? | NC_000913 | = 2515616 | NA (NA) | noncoding (1344/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 3032402 | 120 (1.030) | 3 (0.030) | 3/532 | NT | 2.5% | coding (1036/1449 nt) | uacT | uric acid permease |
| ? | NC_000913 | = 3032405 | 119 (1.050) | coding (1039/1449 nt) | uacT | uric acid permease | |||||