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 | 528,897 | IS5 (+) +4 bp | 42.5% | pseudogene (258‑261/491 nt) | ybbD → | pseudogene |
| RA | 1,097,158 | C→T | 17.3% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,466,210 | G→A | 6.1% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,585 | T→C | 5.6% | pseudogene (1194/2513 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 | 1,708,805 | T→C | 5.9% | R629R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 6.3% | 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 | 1,708,930 | C→A | 8.4% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,958 | T→C | 5.8% | V680V (GTT→GTC) | 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 | 2,304,523 | G→C | 8.1% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,537 | A→G | 8.4% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,540 | C→T | 5.4% | intergenic (+147/+568) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,762 | T→C | 5.0% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| 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 |
| JC | 3,815,859 | Δ82 bp | 89.9% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,532 | A→T | 13.8% | H32L (CAT→CTT) | yidX → | putative lipoprotein |
| RA | 4,116,407 | C→A | 100% | M272I (ATG→ATT) | glpK ← | glycerol kinase |
| RA | 4,183,258 | G→A | 100% | E672K (GAA→AAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 20.2% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 25.6% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 25.4% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 12.0% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 7.2% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 7.5% | 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 |
| JC | 4,396,100 | Δ3 bp | 1.8% | coding (36‑38/1338 nt) | amiB → | N‑acetylmuramoyl‑l‑alanine amidase II |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 527117 | 529137 | 2021 | 67 [64] | [63] 69 | [rhsD]–ybbD | [rhsD], ybbC, rhsH, ybbD |
| * | * | ÷ | NC_000913 | 582640 | 584723 | 2084 | 69 [64] | [62] 71 | [ybcY]–[ompT] | [ybcY], ybcY, tfaX, appY, [ompT] |
| * | * | ÷ | NC_000913 | 1464965 | 1465439 | 475 | 68 [66] | [65] 67 | [paaY]–[ydbA] | [paaY], ynbG, [ydbA] |
| * | * | ÷ | NC_000913 | 1529922 | 1530558 | 637 | 68 [66] | [66] 67 | [rhsE]–[ydcD] | [rhsE], [ydcD] |
| * | * | ÷ | NC_000913 | 1978258 | 1979791 | 1534 | 67 [66] | [66] 69 | insB1–[uspC] | insB1, insA, [uspC] |
| * | * | ÷ | NC_000913 | 2033398 | 2034181 | 784 | 68 [66] | [65] 67 | [yedR]–[yedS] | [yedR], [yedS] |
| * | * | ÷ | NC_000913 | 2105097 | 2107448 | 2352 | 67 [64] | [66] 74 | [wbbI]–[glf] | [wbbI], wbbH, [glf] |
| * | * | ÷ | NC_000913 | 2455522 | 2456217 | 696 | 69 [66] | [64] 67 | [yfcV] | [yfcV] |
| * | * | ÷ | NC_000913 | 2469004 | 2470775 | 1772 | 70 [66] | [65] 67 | [gtrB]–gtrS | [gtrB], gtrS |
| * | * | ÷ | NC_000913 | 2774249 | 2775311 | 1063 | 67 [66] | [66] 67 | [yfjW] | [yfjW] |
| * | * | ÷ | NC_000913 | 2785786 | 2786943 | 1158 | 67 [66] | [66] 68 | [ileY]–[ygaQ] | [ileY], [ygaQ] |
| * | * | ÷ | NC_000913 | 2903539 | 2904114 | 576 | 67 [66] | [64] 70 | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| * | * | ÷ | NC_000913 | 2994854 | 2995999 | 1146 | 67 [60] | [66] 69 | [ygeK]–[ygeO] | [ygeK], ygeN, [ygeN], [ygeO] |
| * | * | ÷ | NC_000913 | 3581611 | 3582293 | 683 | 75 [60] | [65] 68 | [yhhY]–[yhhZ] | [yhhY], [yhhZ] |
| * | * | ÷ | NC_000913 | 3804072 | 3805230 | 1159 | 68 [66] | [64] 67 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4556312 | 4556814 | 503 | 67 [57] | [66] 67 | [yjiC] | [yjiC] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 112281 = | 169 (1.250) | 4 (0.030) | 4/540 | NT | 2.4% | coding (319/744 nt) | zapD | FtsZ stabilizer |
| ? | NC_000913 | 112312 = | 159 (1.200) | coding (288/744 nt) | zapD | FtsZ stabilizer | |||||
| * | ? | NC_000913 | 1207790 = | 79 (0.590) | 58 (0.460) | 49/520 | NT | 47.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 52 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 74 (0.550) | 81 (0.640) | 56/520 | NT | 57.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 52 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1293199 | 137 (1.010) | 4 (0.030) | 4/552 | NT | 2.8% | intergenic (‑277/‑328) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | 1299499 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 22 (0.170) | 20/544 | 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) | 22 (0.170) | 20/536 | 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 | = 3558994 | 37 (0.270) | 99 (0.760) | 66/532 | NT | 70.1% | coding (727/1599 nt) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| ? | NC_000913 | 3560035 = | 49 (0.380) | pseudogene (419/606 nt) | glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon | |||||
| * | ? | NC_000913 | 4409174 = | NA (NA) | 4 (0.030) | 4/522 | NT | 4.0% | noncoding (22/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4409235 = | 95 (0.740) | noncoding (83/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||