mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,834,461 | 0 | G | T | 37.6% | 195.9 / 17.8 | 101 | D116Y (GAT→TAT) | ydjY | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY |
| * | NC_000913 | 2,177,255 | 0 | G | T | 36.2% | 68.8 / 20.6 | 58 | intergenic (‑51/+257) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 1,834,472 | 0 | A | C | 33.0% | 143.9 / 45.1 | 97 | E119D (GAA→GAC) ‡ | ydjY | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY |
| * | NC_000913 | 164,581 | 0 | A | C | 30.4% | 45.6 / 23.7 | 56 | intergenic (+47/‑149) | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | NC_000913 | 1,834,470 | 0 | G | C | 30.0% | 189.0 / 40.8 | 100 | E119Q (GAA→CAA) ‡ | ydjY | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY |
| * | NC_000913 | 4,296,060 | 0 | C | T | 29.7% | 356.2 / 199.6 | 237 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 151,734 | 0 | A | C | 28.9% | 136.1 / 20.6 | 76 | V166V (GTT→GTG) | yadL | putative fimbrial protein YadL |
| * | NC_000913 | 3,608,703 | 0 | A | T | 27.5% | 289.5 / 30.8 | 137 | intergenic (+54/+48) | zntA/tusA | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase/sulfur transfer protein TusA |
| * | NC_000913 | 159,101 | 0 | C | A | 27.1% | 220.9 / 28.7 | 96 | C9F (TGC→TTC) | pcnB | poly(A) polymerase I |
| * | NC_000913 | 361,320 | 0 | C | A | 26.0% | 233.7 / 12.9 | 104 | V181F (GTT→TTT) | lacA | galactoside O‑acetyltransferase |
| * | NC_000913 | 361,311 | 0 | C | A | 25.3% | 203.4 / 11.7 | 100 | E184* (GAA→TAA) | lacA | galactoside O‑acetyltransferase |
| * | NC_000913 | 2,185,429 | 0 | T | G | 25.0% | 115.6 / 14.4 | 60 | intergenic (‑128/+95) | thiM/rcnR | hydroxyethylthiazole kinase/DNA‑binding transcriptional repressor RcnR |
| * | NC_000913 | 2,470,427 | 0 | C | A | 24.5% | 246.3 / 16.6 | 102 | Q433K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 3,391,407 | 0 | A | C | 24.4% | 401.4 / 45.5 | 201 | F208V (TTT→GTT) | tldD | metalloprotease TldD |
| * | NC_000913 | 4,412,781 | 0 | C | G | 24.3% | 184.6 / 19.6 | 77 | S132C (TCT→TGT) | yjfM | DUF1190 domain‑containing protein YjfM |
| * | NC_000913 | 3,504,873 | 0 | T | A | 22.9% | 868.4 / 57.3 | 366 | intergenic (+90/+62) | frlR/yhfS | putative DNA‑binding transcriptional regulator FrlR/putative aminotransferase YhfS |
| * | NC_000913 | 164,579 | 0 | G | C | 22.4% | 130.9 / 12.1 | 58 | intergenic (+45/‑151) | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | NC_000913 | 1,834,430 | 0 | A | T | 22.2% | 268.0 / 12.7 | 109 | A105A (GCA→GCT) | ydjY | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY |
| * | NC_000913 | 4,596,806 | 0 | G | T | 22.1% | 711.3 / 22.6 | 251 | E273* (GAA→TAA) | lgoD | L‑galactonate oxidoreductase |
| * | NC_000913 | 2,229,190 | 0 | T | A | 22.0% | 410.3 / 53.0 | 224 | intergenic (+125/+248) | yohP/dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase |
| Marginal new junction evidence (lowest skew 10 of 309 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 59280 = | 92 (0.690) | 19 (0.160) | 14/264 | 3.0 | 20.6% | intergenic (+1/+407) | yabQ/rluA | protein YabQ/23S rRNA pseudouridine(746) and tRNA pseudouridine(32) synthase |
| ? | NC_000913 | 59320 = | 65 (0.550) | intergenic (+41/+367) | yabQ/rluA | protein YabQ/23S rRNA pseudouridine(746) and tRNA pseudouridine(32) synthase | |||||
| * | ? | NC_000913 | 3423376 = | 130 (0.970) | 18 (0.140) +TTGATGT |
13/284 | 3.3 | 12.5% | intergenic (+182/+47) | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA |
| ? | NC_000913 | 3423672 = | 135 (1.010) | noncoding (116/120 nt) | rrfD | 5S ribosomal RNA | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 29 (0.230) | 12/280 | 3.4 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 286641 = | 561 (4.180) | 12 (0.100) | 9/278 | 3.9 | 2.2% | coding (1247/1383 nt) | yagG | putative D‑xylonate transporter YagG |
| ? | NC_000913 | 286693 = | 566 (4.530) | coding (1299/1383 nt) | yagG | putative D‑xylonate transporter YagG | |||||
| * | ? | NC_000913 | = 4094366 | NA (NA) | 8 (0.080) +37 bp |
6/224 | 4.1 | NA | noncoding (9/36 nt) | other | REP299b |
| ? | NC_000913 | = 4285380 | NA (NA) | intergenic (‑167/+33) | yjcH/acs | conserved inner membrane protein YjcH/acetyl‑CoA synthetase (AMP‑forming) | |||||
| * | ? | NC_000913 | = 3854888 | 425 (3.170) | 15 (0.120) | 8/280 | 4.1 | 3.6% | coding (967/1185 nt) | emrD | multidrug efflux pump EmrD |
| ? | NC_000913 | = 3854930 | 396 (3.140) | coding (1009/1185 nt) | emrD | multidrug efflux pump EmrD | |||||
| * | ? | NC_000913 | 315563 = | NA (NA) | 9 (0.070) | 8/278 | 4.1 | NA | noncoding (335/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315599 = | NA (NA) | noncoding (371/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 3620220 | NA (NA) | 10 (0.080) | 8/286 | 4.2 | 100% | coding (1029/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3620255 | 0 (0.000) | coding (1064/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 730643 | 291 (2.170) | 10 (0.080) | 8/292 | 4.2 | 3.4% | coding (1061/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | = 3620223 | NA (NA) | coding (1032/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 284691 | 790 (5.890) | 15 (0.110) | 8/290 | 4.2 | 1.9% | coding (1491/1968 nt) | yagF | CP4‑6 prophage; D‑xylonate dehydratase |
| ? | NC_000913 | = 284723 | 745 (5.710) | coding (1523/1968 nt) | yagF | CP4‑6 prophage; D‑xylonate dehydratase | |||||