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 45 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 2,488,700 | 0 | G | A | 35.0% | 134.6 / 31.1 | 80 | S29L (TCA→TTA) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 1,437,441 | 0 | G | A | 32.9% | 124.5 / 34.6 | 70 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 3,004,668 | 0 | C | T | 32.0% | 194.7 / 30.1 | 97 | intergenic (‑226/‑253) | Y75_RS14955/ygeW | sigma‑54‑dependent transcriptional regulator/knotted carbamoyltransferase YgeW |
| * | NC_007779 | 2,004,055 | 0 | A | C | 31.8% | 183.8 / 20.5 | 88 | intergenic (‑129/+192) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 2,850,310 | 0 | T | G | 31.7% | 114.1 / 19.5 | 60 | G218G (GGT→GGG) | hypB | hydrogenase nickel incorporation protein HypB |
| * | NC_007779 | 3,205,102 | 0 | C | A | 30.8% | 72.7 / 12.8 | 53 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 658,098 | 0 | A | C | 30.6% | 138.4 / 15.8 | 72 | V88G (GTG→GGG) | crcB | fluoride efflux transporter CrcB |
| * | NC_007779 | 1,437,432 | 0 | G | A | 30.3% | 133.5 / 24.7 | 66 | intergenic (‑99/+42) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 2,488,707 | 0 | C | A | 29.5% | 166.1 / 17.3 | 78 | A27S (GCG→TCG) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 4,609,024 | 0 | C | T | 29.0% | 127.6 / 25.3 | 69 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 3,401,314 | 0 | T | C | 28.9% | 157.9 / 20.0 | 76 | D625G (GAT→GGT) | csrD | RNase E specificity factor CsrD |
| * | NC_007779 | 3,908,691 | 0 | C | T | 28.8% | 165.0 / 12.8 | 73 | L198L (TTG→TTA) | Y75_RS19370 | D‑xylose ABC transporter substrate‑binding protein |
| * | NC_007779 | 1,437,435 | 0 | T | A | 27.5% | 165.6 / 19.0 | 69 | intergenic (‑102/+39) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 3,205,091 | 0 | C | T | 26.9% | 86.6 / 18.1 | 52 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 29,486 | 0 | C | A | 26.9% | 193.0 / 19.0 | 67 | intergenic (+291/‑165) | dapB/Y75_RS00165 | 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit |
| * | NC_007779 | 29,496 | 0 | T | A | 26.4% | 180.2 / 24.2 | 72 | intergenic (+301/‑155) | dapB/Y75_RS00165 | 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit |
| * | NC_007779 | 1,989,132 | 0 | A | C | 26.4% | 161.8 / 10.7 | 72 | Y24S (TAC→TCC) | Y75_RS10015 | non‑heme ferritin‑like protein |
| * | NC_007779 | 1,097,580 | 0 | C | T | 26.2% | 99.1 / 38.9 | 61 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 4,291,309 | 0 | T | A | 25.8% | 158.2 / 26.5 | 66 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 3,004,670 | 0 | G | T | 25.5% | 258.7 / 23.2 | 94 | intergenic (‑228/‑251) | Y75_RS14955/ygeW | sigma‑54‑dependent transcriptional regulator/knotted carbamoyltransferase YgeW |
| 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) | 53 (0.540) | 44/498 | 3.4 | 93.0% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 4 (0.040) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 4547370 | 91 (0.920) | 22 (0.230) | 21/480 | 8.2 | 19.2% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 97 (1.020) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | 4547362 = | 88 (0.890) | 15 (0.160) | 15/480 | 10.4 | 14.0% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 100 (1.050) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 2069490 | 109 (1.100) | 48 (0.490) | 11/498 | 12.6 | 45.9% | intergenic (‑32/+1) | Y75_RS10470/Y75_RS24935 | IS5‑like element IS5 family transposase/hypothetical protein |
| ? | NC_007779 | = 4540919 | 4 (0.040) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||