mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 50 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 3,004,668 | 0 | C | T | 37.5% | 111.7 / 35.8 | 72 | intergenic (‑226/‑253) | Y75_RS14955/ygeW | sigma‑54‑dependent transcriptional regulator/knotted carbamoyltransferase YgeW |
| * | NC_007779 | 1,097,580 | 0 | C | T | 36.1% | 73.7 / 73.6 | 72 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 4,291,309 | 0 | T | A | 32.4% | 127.5 / 37.4 | 68 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 627,875 | 0 | T | G | 31.2% | 131.4 / 10.8 | 64 | G34G (GGT→GGG) | dhbA | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| * | NC_007779 | 4,609,024 | 0 | C | T | 31.2% | 145.4 / 28.1 | 80 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 2,488,700 | 0 | G | A | 30.7% | 207.9 / 30.0 | 101 | S29L (TCA→TTA) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 753,547 | 0 | T | A | 29.8% | 177.4 / 31.2 | 84 | intergenic (‑330/+60) | Y75_RS03720/gltA | type 1 fimbrial protein/citrate (Si)‑synthase |
| * | NC_007779 | 2,331,120 | 0 | T | G | 29.5% | 114.9 / 20.9 | 62 | G114G (GGT→GGG) | Y75_RS11690 | acetyl‑CoA acetyltransferase |
| * | NC_007779 | 1,826,775 | 0 | G | A | 28.8% | 157.6 / 27.4 | 73 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 3,176,404 | 0 | C | A | 28.2% | 179.9 / 32.1 | 85 | E55* (GAG→TAG) | nudF | ADP‑ribose diphosphatase |
| * | NC_007779 | 1,097,540 | 0 | C | A | 26.9% | 116.0 / 22.3 | 52 | intergenic (+289/+85) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 3,205,091 | 0 | C | T | 26.7% | 166.3 / 40.7 | 90 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 3,974,713 | 0 | G | T | 26.7% | 201.8 / 16.7 | 76 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NC_007779 | 1,294,035 | 0 | T | A | 25.8% | 236.3 / 30.9 | 97 | intergenic (+93/+51) | galU/hns | UTP‑‑glucose‑1‑phosphate uridylyltransferase GalU/DNA‑binding transcriptional regulator H‑NS |
| * | NC_007779 | 127,209 | 0 | T | G | 25.6% | 192.6 / 14.9 | 86 | G505G (GGT→GGG) | aceF | pyruvate dehydrogenase complex dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_007779 | 3,189,759 | 0 | C | T | 25.5% | 222.7 / 23.2 | 95 | P158S (CCA→TCA) | Y75_RS15860 | fimbrial protein |
| * | NC_007779 | 1,581,471 | 0 | C | A | 25.2% | 265.6 / 29.3 | 103 | C345F (TGC→TTC) | Y75_RS07900 | anaerobic sulfatase maturase |
| * | NC_007779 | 29,496 | 0 | T | A | 24.7% | 195.4 / 24.8 | 77 | intergenic (+301/‑155) | dapB/Y75_RS00165 | 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit |
| * | NC_007779 | 2,488,707 | 0 | C | A | 24.5% | 262.3 / 14.1 | 102 | A27S (GCG→TCG) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 2,902,348 | 0 | C | A | 24.3% | 184.8 / 31.8 | 70 | intergenic (+318/+1055) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 60 (0.560) | 50/498 | 3.4 | 96.8% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 2 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 381401 = | NA (NA) | 48 (0.450) | 42/494 | 4.6 | NA | coding (512/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 381812 | NA (NA) | pseudogene (174/174 nt) | Y75_RS23175 | acetyltransferase | |||||
| * | ? | NC_007779 | = 4547370 | 113 (1.050) | 21 (0.200) | 21/480 | 9.6 | 17.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 86 (0.830) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | 4547362 = | 106 (0.980) | 16 (0.150) | 16/480 | 11.5 | 14.5% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 87 (0.840) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 2069490 | 107 (0.990) | 57 (0.530) | 11/498 | 14.3 | 51.1% | intergenic (‑32/+1) | Y75_RS10470/Y75_RS24935 | IS5‑like element IS5 family transposase/hypothetical protein |
| ? | NC_007779 | = 4540919 | 2 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||