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 |
| JC | 167,126 | Δ3 bp | 2.2% | coding (2397‑2399/2535 nt) | mrcB → | fused glycosyl transferase and transpeptidase |
| RA | 1,004,713 | C→T | 5.8% | intergenic (+56/‑55) | ycbF → / → pyrD | putative periplasmic pilin chaperone/dihydro‑orotate oxidase, FMN‑linked |
| RA | 1,097,158 | C→T | 12.8% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| JC JC | 1,293,124 | IS5 (+) +4 bp | 13.7% | intergenic (‑202/‑400) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,466,201 | T→C | 5.7% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,713 | C→A | 7.8% | pseudogene (1322/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 5.8% | pseudogene (1338/2513 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 |
| JC | 1,557,539 | Δ3 bp | 3.0% | coding (498‑500/927 nt) | ddpF ← | D,D‑dipeptide ABC transporter ATPase |
| RA | 1,708,844 | C→G | 9.5% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,890,799 | A→G | 5.2% | S157P (TCC→CCC) | tsaB ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; binding partner and protease for TsaD |
| 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 | 6.3% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,537 | A→G | 5.8% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,748 | T→G | 6.5% | intergenic (+355/+360) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,762 | T→C | 8.3% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,798 | T→C | 12.9% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,988 | T→C | 9.5% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,013 | A→G | 7.0% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,942,306 | G→T | 5.7% | Q88K (CAG→AAG) | gcvA ← | glycine cleavage system transcriptional activator; autorepressor |
| 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 | 3,560,460 | A→T | 6.2% | pseudogene (146/150 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,815,809 | Δ1 bp | 62.2% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 5.4% | [rph]–[rph] | [rph], [rph] | |
| RA | 4,116,407 | C→A | 94.1% | 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 | 20.8% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 21.1% | 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 | 23.1% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 11.9% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 14.4% | 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 | 238049 | 238820 | 772 | 48 [47] | [47] 48 | [yafT]–[yafU] | [yafT], ykfM, [yafU] |
| * | * | ÷ | NC_000913 | 522736 | 523301 | 566 | 48 [45] | [47] 49 | [ybbP]–[rhsD] | [ybbP], [rhsD] |
| * | * | ÷ | NC_000913 | 582727 | 584740 | 2014 | 48 [47] | [46] 49 | [ybcY]–[ompT] | [ybcY], ybcY, tfaX, appY, [ompT] |
| * | * | ÷ | NC_000913 | 720795 | 721179 | 385 | 50 [43] | [47] 48 | [ybfK]–[kdpE] | [ybfK], [kdpE] |
| * | * | ÷ | NC_000913 | 1211022 | 1212804 | 1783 | 48 [47] | [47] 49 | [mcrA]–[ycgX] | [mcrA], icdC, iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1640567 | 1641247 | 681 | 48 [47] | [46] 48 | [essQ] | [essQ] |
| * | * | ÷ | NC_000913 | 1754585 | 1755493 | 909 | 48 [46] | [47] 48 | ydhZ | ydhZ |
| * | * | ÷ | NC_000913 | 1812581 | 1813380 | 800 | 49 [47] | [47] 48 | [ydjO] | [ydjO] |
| * | * | ÷ | NC_000913 | 1978296 | 1979748 | 1453 | 49 [45] | [44] 49 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2056562 | 2056913 | 352 | 49 [45] | [46] 48 | [yeeN] | [yeeN] |
| * | * | ÷ | NC_000913 | 2068293 | 2068713 | 421 | 48 [45] | [47] 48 | [yoeH]–[yoeA] | [yoeH], [yoeA] |
| * | * | ÷ | NC_000913 | 2103300 | 2104281 | 982 | 48 [47] | [47] 48 | [wbbL]–[wbbK] | [wbbL], [wbbK] |
| * | * | ÷ | NC_000913 | 2385611 | 2386062 | 452 | 48 [47] | [46] 48 | [yfbK]–[yfbL] | [yfbK], [yfbL] |
| * | * | ÷ | NC_000913 | 2469059 | 2470743 | 1685 | 48 [47] | [44] 52 | [gtrB]–gtrS | [gtrB], gtrS |
| * | * | ÷ | NC_000913 | 2774147 | 2775442 | 1296 | 49 [47] | [45] 51 | [yfjW] | [yfjW] |
| * | * | ÷ | NC_000913 | 2784358 | 2786803 | 2446 | 48 [46] | [47] 48 | [ypjC]–[ygaQ] | [ypjC], ileY, [ygaQ] |
| * | * | ÷ | NC_000913 | 2884176 | 2884574 | 399 | 49 [46] | [47] 48 | [ygcB] | [ygcB] |
| * | * | ÷ | NC_000913 | 2994952 | 2996024 | 1073 | 48 [47] | [47] 48 | [ygeK]–[ygeO] | [ygeK], ygeN, ygeN, [ygeO] |
| * | * | ÷ | NC_000913 | 3252597 | 3253062 | 466 | 50 [47] | [45] 50 | [yhaH]–[yhaI] | [yhaH], [yhaI] |
| * | * | ÷ | NC_000913 | 3267922 | 3269738 | 1817 | 49 [46] | [45] 48 | [yhaB]–yhaC | [yhaB], yhaC |
| * | * | ÷ | NC_000913 | 3286996 | 3287498 | 503 | 49 [46] | [47] 50 | [agaI]–[yraH] | [agaI], [yraH] |
| * | * | ÷ | NC_000913 | 3413500 | 3413746 | 247 | 48 [44] | [47] 49 | acrS/acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| * | * | ÷ | NC_000913 | 3652192–3653236 | 3654046 | 811–1855 | 48 [47] | [47] 49 | [insH1]–[slp] | [insH1], yhiS, [slp] |
| * | * | ÷ | NC_000913 | 3769396 | 3770262 | 867 | 48 [47] | [47] 48 | [yibV]–[yibH] | [yibV], yibV, yibU, yibU, [yibH] |
| * | * | ÷ | NC_000913 | 3796873 | 3798473 | 1601 | 49 [47] | [45] 49 | [waaC]–[waaU] | [waaC], waaL, [waaU] |
| * | * | ÷ | NC_000913 | 3798480 | 3800577 | 2098 | 49 [41] | [46] 48 | [waaU]–[waaY] | [waaU], waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 3800712 | 3801402 | 691 | 49 [47] | [47] 48 | [waaY]–[waaR] | [waaY], [waaR] |
| * | * | ÷ | NC_000913 | 3804072 | 3805216 | 1145 | 49 [46] | [47] 49 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4409988 | 4410291 | 304 | 48 [44] | [47] 48 | [rlmB]–[yjfI] | [rlmB], [yjfI] |
| * | * | ÷ | NC_000913 | 4476508 | 4477258 | 751 | 48 [47] | [47] 48 | [yjgL] | [yjgL] |
| * | * | ÷ | NC_000913 | 4556286 | 4556746 | 461 | 49 [42] | [46] 49 | [yjiC] | [yjiC] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 90 (0.910) | 68/532 | NT | 100% | intergenic (+8/‑769) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers | |||||
| * | ? | NC_000913 | = 609351 | NA (NA) | 5 (0.050) | 5/540 | NT | 4.8% | noncoding (1345/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 1896966 = | 97 (0.980) | coding (35/1365 nt) | sdaA | L‑serine dehydratase 1 | |||||
| * | ? | NC_000913 | 1207790 = | 48 (0.470) | 57 (0.590) | 47/516 | NT | 57.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 38 (0.390) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 46 (0.450) | 45 (0.470) | 41/516 | NT | 52.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 38 (0.390) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293196 = | 82 (0.800) | 6 (0.060) | 6/548 | NT | 6.8% | intergenic (‑274/‑331) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 19 (0.190) | 17/540 | NT | 97.5% | 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 | = 1896969 | 91 (0.920) | 4 (0.040) | 4/540 | NT | 4.2% | coding (38/1365 nt) | sdaA | L‑serine dehydratase 1 |
| ? | NC_000913 | 2514273 = | NA (NA) | noncoding (1/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 13 (0.130) | 13/532 | 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 | 2325648 = | 107 (1.050) | 3 (0.030) | 3/536 | NT | 2.8% | coding (893/1323 nt) | atoE | short chain fatty acid transporter |
| ? | NC_000913 | 2325669 = | 104 (1.040) | coding (914/1323 nt) | atoE | short chain fatty acid transporter | |||||
| * | ? | NC_000913 | = 3042067 | 121 (1.180) | 5 (0.050) | 5/536 | NT | 4.0% | coding (755/981 nt) | ygfZ | iron‑sulfur cluster repair protein, plumbagin resistance |
| ? | NC_000913 | = 3042074 | 123 (1.230) | coding (762/981 nt) | ygfZ | iron‑sulfur cluster repair protein, plumbagin resistance | |||||