mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 250 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,001,918 | 0 | A | C | 49.1% | 91.5 / 11.9 | 59 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin) |
| * | NC_000913 | 2,378,968 | 0 | C | T | 46.7% | 17.6 / 21.1 | 46 | E98K (GAA→AAA) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| * | NC_000913 | 3,665,702 | 0 | C | A | 46.1% | 83.5 / 54.5 | 76 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 2,619,230 | 0 | T | C | 46.0% | 65.1 / 11.5 | 50 | I311V (ATT→GTT) | uraA | uracil permease |
| * | NC_000913 | 646,747 | 0 | T | G | 45.9% | 91.9 / 13.9 | 61 | T255P (ACC→CCC) | citG | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| * | NC_000913 | 1,736,789 | 0 | G | C | 45.5% | 62.2 / 13.2 | 44 | L168V (CTG→GTG) | ydhP | putative MFS transporter, inner membrane protein |
| * | NC_000913 | 3,595,044 | 0 | T | A | 45.2% | 40.8 / 21.0 | 42 | Y146F (TAC→TTC) | livM | branched‑chain amino acid ABC transporter permease |
| * | NC_000913 | 689,514 | 0 | A | C | 43.2% | 56.1 / 11.5 | 37 | G456G (GGT→GGG) | lnt | apolipoprotein N‑acyltransferase |
| * | NC_000913 | 589,934 | 0 | T | G | 42.9% | 50.7 / 10.6 | 36 | T341P (ACC→CCC) | nfrA | bacteriophage N4 receptor, outer membrane subunit |
| * | NC_000913 | 599,576 | 0 | T | G | 42.1% | 87.1 / 26.4 | 57 | V288G (GTG→GGG) | cusA | copper/silver efflux system, membrane component |
| * | NC_000913 | 2,984,441 | 0 | A | C | 41.5% | 95.3 / 17.8 | 54 | G384G (GGT→GGG) | yqeF | short chain acyltransferase |
| * | NC_000913 | 925,900 | 0 | A | G | 41.2% | 87.5 / 14.1 | 52 | noncoding (72/88 nt) | serW | tRNA‑Ser |
| * | NC_000913 | 2,337,723 | 0 | A | C | 40.8% | 75.3 / 12.5 | 50 | G566G (GGT→GGG) | gyrA | DNA gyrase (type II topoisomerase), subunit A |
| * | NC_000913 | 1,574,051 | 0 | G | T | 40.7% | 93.3 / 22.1 | 54 | V384V (GTC→GTA) | pqqL | putative periplasmic M16 family zinc metalloendopeptidase |
| * | NC_000913 | 2,532,988 | 0 | G | A | 40.5% | 53.7 / 18.9 | 43 | G194S (GGC→AGC) | cysK | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit |
| * | NC_000913 | 646,777 | 0 | G | T | 40.4% | 68.5 / 27.8 | 52 | Q245K (CAA→AAA) | citG | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| * | NC_000913 | 3,508,662 | 0 | T | A | 40.4% | 81.1 / 19.5 | 57 | E384D (GAA→GAT) | yhfW | phosphopentomutase‑related metalloenzyme superfamily protein |
| * | NC_000913 | 3,026,941 | 0 | A | C | 40.0% | 89.8 / 10.6 | 50 | E392D (GAA→GAC) | guaD | guanine deaminase |
| * | NC_000913 | 4,067,745 | 0 | A | G | 39.7% | 99.8 / 11.5 | 58 | L511P (CTG→CCG) | yihQ | putative sulpholipid alpha‑glucosidase; alpha‑glucosyl fluoride glucosidase |
| * | NC_000913 | 2,676,106 | 0 | C | A | 39.6% | 70.8 / 25.4 | 53 | L240F (TTG→TTT) | yphD | putative sugar ABC transporter permease |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 780631 | 0 (0.000) | 22 (0.420) | 16/258 | 4.2 | 53.0% | intergenic (+2/‑134) | lysT/valT | tRNA‑Lys/tRNA‑Val |
| ? | NC_000913 | 2521487 = | 39 (0.740) | intergenic (+159/+106) | lysV/xapR | tRNA‑Lys/transcriptional activator of xapAB | |||||
| * | ? | NC_000913 | = 780631 | 0 (0.000) | 21 (0.400) | 11/258 | 5.9 | 41.6% | intergenic (+2/‑134) | lysT/valT | tRNA‑Lys/tRNA‑Val |
| ? | NC_000913 | 781811 = | 59 (1.120) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | NC_000913 | = 4542690 | 75 (1.230) | 3 (0.050) | 3/280 | 11.1 | 3.9% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 78 (1.360) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4542682 = | 81 (1.330) | 3 (0.050) | 3/280 | 11.1 | 3.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 78 (1.360) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 1615598 = | 67 (1.100) | 3 (0.050) | 3/286 | 11.3 | 4.8% | coding (795/882 nt) | yneJ | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | = 1625301 | 54 (0.920) | intergenic (+10/+34) | ydeJ/dcp | inactive PncC family protein/dipeptidyl carboxypeptidase II | |||||