mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 266 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,297,496 | 0 | G | A | 58.4% | 251.7 / inf | 479 | A209V (GCT→GTT) | adhE | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| * | NC_000913 | 3,585,517 | 0 | G | A | 57.1% | 206.5 / inf | 521 | A436V (GCC→GTC) | ggt | gamma‑glutamyltranspeptidase |
| * | NC_000913 | 1,282,627 | 0 | C | T | 56.8% | 197.1 / inf | 465 | Q922* (CAG→TAG) | narG | nitrate reductase 1, alpha subunit |
| * | NC_000913 | 4,303,755 | 0 | C | T | 56.3% | 172.3 / inf | 486 | V119I (GTT→ATT) | mdtN | membrane fusion protein of efflux pump |
| * | NC_000913 | 3,589,956 | 0 | G | A | 56.1% | 158.5 / inf | 461 | L24L (CTC→CTT) | ugpE | sn‑glycerol‑3‑phosphate ABC transporter permease |
| * | NC_000913 | 3,061,916 | 0 | C | T | 55.5% | 138.9 / inf | 509 | A356V (GCC→GTC) | scpA | methylmalonyl‑CoA mutase |
| * | NC_000913 | 283,338 | 0 | G | A | 55.5% | 141.3 / inf | 476 | M46I (ATG→ATA) | yagF | CP4‑6 prophage; dehydratase family protein |
| * | NC_000913 | 4,320,079 | 0 | C | T | 55.5% | 138.7 / inf | 467 | Q195Q (CAG→CAA) | phnI | ribophosphonate triphosphate synthase complex putative catalytic subunit |
| * | NC_000913 | 3,560,119 | 0 | A | G | 55.1% | 237.4 / inf | 499 | pseudogene (335/606 nt) | glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| * | NC_000913 | 4,282,536 | 0 | C | T | 55.1% | 187.9 / inf | 604 | Q180Q (CAG→CAA) | yjcF | pentapeptide repeats protein |
| * | NC_000913 | 2,329,209 | 0 | A | G | 55.0% | 210.2 / inf | 478 | W197R (TGG→CGG) | yfaQ | tandem DUF2300 domain protein, putative host defense protein |
| * | NC_000913 | 3,132,077 | 0 | G | A | 54.7% | 117.5 / inf | 529 | A111V (GCG→GTG) | yghQ | putative inner membrane polysaccharide flippase |
| * | NC_000913 | 340,202 | 0 | G | A | 54.6% | 135.6 / inf | 505 | S13N (AGC→AAC) | yahI | carbamate kinase‑like protein |
| * | NC_000913 | 1,306,736 | 0 | T | G | 54.6% | 267.7 / inf | 457 | S325A (TCC→GCC) | oppF | oligopeptide ABC transporter ATPase |
| * | NC_000913 | 290,175 | 0 | G | A | 54.4% | 108.4 / inf | 537 | T44I (ACC→ATC) | argF | ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| * | NC_000913 | 3,256,157 | 0 | C | T | 54.4% | 73.9 / inf | 401 | Q165Q (CAG→CAA) | yhaM | putative L‑serine dehydratase alpha chain |
| * | NC_000913 | 4,407,045 | 0 | C | T | 54.3% | 90.6 / inf | 532 | A131V (GCT→GTT) | rnr | exoribonuclease R, RNase R |
| * | NC_000913 | 1,994,637 | 0 | A | G | 54.3% | 201.9 / inf | 500 | Y24H (TAC→CAC) | uvrC | excinuclease UvrABC, endonuclease subunit |
| * | NC_000913 | 3,558,291 | 0 | C | T | 54.2% | 107.9 / inf | 487 | G8G (GGC→GGT) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| * | NC_000913 | 4,325,837 | 0 | C | T | 54.1% | 90.6 / inf | 584 | intergenic (‑96/+562) | yjdN/yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| Marginal new junction evidence (lowest skew 10 of 94 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 276 (0.550) | 173/300 | 3.1 | 45.9% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4542042 = | 326 (0.650) | coding (6/597 nt) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 462 (0.920) | 170/300 | 3.4 | 63.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 577188 = | 266 (0.530) | intergenic (‑363/‑210) | nmpC/essD | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein | |||||
| * | ? | NC_000913 | = 3964579 | 286 (0.570) | 251 (0.520) | 162/290 | 3.7 | 47.6% | coding (1052/1266 nt) | rhlB | ATP‑dependent RNA helicase |
| ? | NC_000913 | 3964586 = | 277 (0.570) | coding (1045/1266 nt) | rhlB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | 677185 = | 302 (0.600) | 240 (0.510) | 156/284 | 4.0 | 45.9% | coding (475/708 nt) | ybeR | uncharacterized protein |
| ? | NC_000913 | = 677214 | 281 (0.590) | coding (504/708 nt) | ybeR | uncharacterized protein | |||||
| * | ? | NC_000913 | = 1095502 | NA (NA) | 256 (0.510) | 163/298 | 4.1 | 46.2% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 1199871 | 298 (0.600) | coding (936/1128 nt) | intE | e14 prophage; putative integrase | |||||
| * | ? | NC_000913 | 1399590 = | 333 (0.660) | 311 (0.620) | 163/300 | 4.3 | 48.3% | intergenic (‑64/+131) | fnr/ogt | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3815858 | 258 (0.510) | 227 (0.480) | 151/280 | 4.4 | 47.5% | pseudogene (24/48 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| ? | NC_000913 | 3815941 = | 260 (0.560) | pseudogene (609/669 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 273 (0.540) | 162/300 | 4.4 | NA | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4434636 | NA (NA) | coding (1930/1944 nt) | cpdB | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase | |||||
| * | ? | NC_000913 | = 1399593 | 335 (0.670) | 371 (0.740) | 161/298 | 4.4 | 52.5% | intergenic (‑67/+128) | fnr/ogt | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 261 (0.520) | 162/300 | 4.4 | 44.5% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4542042 = | 326 (0.650) | coding (6/597 nt) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA | |||||