mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 47,839 | T→C | 2.7% | V24A (GTA→GCA) | kefC → | potassium:proton antiporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 357,922 | C→G | 7.5% | A257P (GCC→CCC) | cynR ← | transcriptional activator of cyn operon, autorepressor |
| RA | 552,526 | T→C | 3.1% | L23L (TTA→TTG) | purK ← | N5‑carboxyaminoimidazole ribonucleotide synthase |
| RA | 884,387 | A→G | 9.6% | I239V (ATC→GTC) | mdfA → | multidrug efflux system protein |
| RA | 974,759 | T→G | 9.1% | G147G (GGT→GGG) | mukF → | chromosome condensin MukBEF, kleisin‑like subunit, binds calcium |
| RA | 1,004,628 | A→G | 6.9% | S228G (AGT→GGT) | ycbF → | putative periplasmic pilin chaperone |
| RA | 1,040,034 | G→T | 2.9% | V247L (GTG→TTG) | cbdB → | cytochrome bd‑II oxidase, subunit II |
| RA | 1,051,413 | G→T | 2.6% | intergenic (‑238/‑48) | cspH ← / → cspG | stress protein, member of the CspA‑family/cold shock protein homolog, cold‑inducible |
| RA | 1,417,463 | Δ1 bp | 2.7% | intergenic (‑77/+25) | recE ← / ← racC | Rac prophage, exonuclease VIII, 5' to 3' specific dsDNA exonuclease/Rac prophage, uncharacterized protein |
| RA | 1,466,201 | T→C | 3.2% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,708,758 | G→C | 5.7% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,714,911 | G→A | 3.1% | A179T (GCA→ACA) | gstA → | glutathionine S‑transferase |
| RA | 2,009,317 | G→A | 2.6% | A347A (GCG→GCA) | yedE → | UPF0394 family sulphur transport domain‑containing inner membrane protein |
| RA | 2,066,465 | T→C | 36.9% | K286R (AAG→AGG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,131,514 | T→C | 7.6% | E186G (GAG→GGG) | wcaC ← | putative glycosyl transferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,162,088 | G→A | 2.5% | V209I (GTA→ATA) | iceT → | putative citrate/iron‑citrate/zinc‑citrate efflux transporter |
| RA | 2,304,535 | A→G | 4.5% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,796 | T→C | 10.4% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,528,973 | T→C | 7.2% | E401G (GAG→GGG) | ligA ← | DNA ligase, NAD(+)‑dependent |
| RA | 3,059,273 | A→G | 2.9% | Y17Y (TAT→TAC) | rpiA ← | ribose 5‑phosphate isomerase, constitutive |
| RA | 3,099,445 | T→C | 2.6% | H40R (CAC→CGC) | yggM ← | DUF1202 family putative secreted protein |
| RA | 3,154,352 | T→G | 3.4% | S289R (AGC→CGC) | yqhC ← | transcriptional activator of yqhD |
| RA | 3,154,358 | A→T | 2.9% | Y287N (TAT→AAT) | yqhC ← | transcriptional activator of yqhD |
| RA | 3,154,359 | G→A | 3.8% | G286G (GGC→GGT) | yqhC ← | transcriptional activator of yqhD |
| RA | 3,154,362 | G→A | 3.3% | V285V (GTC→GTT) ‡ | yqhC ← | transcriptional activator of yqhD |
| RA | 3,154,364 | C→A | 2.8% | V285F (GTC→TTC) ‡ | yqhC ← | transcriptional activator of yqhD |
| RA | 3,275,505 | G→A | 2.7% | A76T (GCC→ACC) | garD → | D‑galactarate dehydrogenase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,524 | G→T | 4.9% | V30F (GTT→TTT) | yidX → | putative lipoprotein |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,160 | T→C | 7.6% | L189P (CTC→CCC) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,295,833 | T→C | 6.3% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 11.4% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 43.2% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 43.9% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,572,447 | A→T | 2.9% | pseudogene (33/1503 nt) | yjiT → | pseudogene |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4233736 | 4235520 | 1785 | 74 [71] | [71] 73 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 171 (0.880) | 98/478 | NT | 98.8% | intergenic (+9/‑768) | 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 | = 1293039 | 2 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1049778 = | 152 (0.780) | 18 (0.090) | 3/478 | NT | 14.9% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | NC_000913 | = 4507640 | 53 (0.270) | coding (979/1152 nt) | insI1 | IS30 transposase | |||||
| * | ? | NC_000913 | 1207790 = | 43 (0.220) | 136 (0.750) | 83/446 | NT | 79.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 29 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 42 (0.220) | 149 (0.820) | 92/446 | NT | 81.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 29 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 5 (0.030) | 165 (0.850) | 89/478 | NT | 97.1% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 70 (0.370) | 55/470 | 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) | 76 (0.400) | 46/462 | 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 | 1979486 = | 0 (0.000) | 81 (0.420) | 52/478 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 156 (0.800) | 81/478 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2070250 = | 110 (0.560) | 3 (0.020) | 3/460 | NT | 2.6% | intergenic (‑70/‑27) | insC1/yoeA | IS2 repressor TnpA/CP4‑44 prophage, putative disrupted hemin or colicin receptor,Phage or Prophage Related, interrupted by IS2 and C‑terminal deletion |
| ? | NC_000913 | 2070480 = | 118 (0.630) | intergenic (+6/‑180) | yoeA/yeeP | CP4‑44 prophage, putative disrupted hemin or colicin receptor,Phage or Prophage Related, interrupted by IS2 and C‑terminal deletion/pseudogene, CP4‑44 prophage, 50S ribosome‑binding GTPase family,Phage or Prophage Related, putative histone | |||||
| * | ? | NC_000913 | = 3154351 | 160 (0.820) | 6 (0.030) | 5/460 | NT | 3.8% | coding (866/957 nt) | yqhC | transcriptional activator of yqhD |
| ? | NC_000913 | = 3154364 | 154 (0.820) | coding (853/957 nt) | yqhC | transcriptional activator of yqhD | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 19 (0.120) | 4/400 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | 4542683 = | 38 (0.190) | 6 (0.030) | 6/460 | NT | 7.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542997 = | 123 (0.660) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||