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 | 20.2% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 15.9% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 1,311,197 | G→T | 17.9% | E37* (GAA→TAA) | tonB → | membrane spanning protein in TonB‑ExbB‑ExbD transport complex |
| RA | 1,466,711 | T→C | 7.2% | 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 | 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 |
| RA | 1,679,869 | A→T | 6.6% | I105F (ATC→TTC) | ydgI → | putative arginine/ornithine antiporter transporter |
| RA | 1,708,765 | T→A | 8.4% | V616D (GTC→GAC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,756,457 | +A | 80.0% | coding (760/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,796,524 | A→G | 6.0% | I474T (ATC→ACC) | pheT ← | phenylalanine tRNA synthetase, beta subunit |
| 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 | 10.4% | L83V (CTT→GTT) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 2,173,359 | Δ1 bp | 7.4% | pseudogene (4/442 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 | 2,173,360 | Δ1 bp | 7.4% | 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 | 2,966,582 | C→T | 80.4% | G618D (GGC→GAC) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,440,065 | G→A | 12.6% | P322L (CCA→CTA) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,560,455 | +G | 93.8% | 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 | 4,296,190 | A→G | 24.7% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 33.4% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 23.7% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 17.2% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 9.8% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +C | 92.7% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +G | 92.7% | 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 | 1211045 | 1212812 | 1768 | 47 [45] | [45] 46 | [mcrA]–[ycgX] | [mcrA], icdC, iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1978373 | 1979728 | 1356 | 47 [41] | [45] 46 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2469052 | 2470736 | 1685 | 47 [44] | [43] 48 | [gtrB]–gtrS | [gtrB], gtrS |
| * | * | ÷ | NC_000913 | 3267939 | 3269705 | 1767 | 46 [44] | [45] 46 | [yhaB]–yhaC | [yhaB], yhaC |
| * | * | ÷ | NC_000913 | 4002599 | 4003407 | 809 | 48 [44] | [45] 46 | [yigF]–[rarD] | [yigF], yigG, [rarD] |
| * | * | ÷ | NC_000913 | 4476521 | 4477228 | 708 | 50 [34] | [45] 47 | 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 | 1207790 = | 55 (0.540) | 30 (0.310) | 26/516 | NT | 39.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 41 (0.430) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 48 (0.470) | 28 (0.290) | 24/516 | NT | 39.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 41 (0.430) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 24 (0.240) | 19/540 | 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) | 23 (0.230) | 17/532 | 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 | 3194098 = | 100 (0.980) | 3 (0.030) | 3/536 | NT | 3.0% | coding (1235/1662 nt) | yqiK | PHB family membrane protein, function unknown |
| ? | NC_000913 | 3194119 = | 98 (0.980) | coding (1256/1662 nt) | yqiK | PHB family membrane protein, function unknown | |||||