mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,097,118 | 0 | C | A | 45.8% | ‑4.2 / 25.7 | 24 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,911,533 | 0 | C | A | 38.3% | 188.8 / 35.9 | 154 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 58,065 | 0 | C | A | 37.1% | 95.8 / 11.2 | 62 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 847,955 | 0 | G | A | 36.5% | 63.6 / 25.8 | 65 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,626,064 | 0 | C | A | 33.8% | 116.0 / 10.2 | 75 | L51L (CTC→CTA) | radA | DNA recombination protein |
| * | NC_000913 | 12,152 | 0 | G | T | 32.6% | 137.3 / 14.1 | 95 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 4,296,268 | 0 | T | C | 30.8% | 56.0 / 18.2 | 39 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,360,965 | 0 | C | A | 30.1% | 209.9 / 11.2 | 113 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 141,849 | 0 | C | A | 29.9% | 170.2 / 13.6 | 87 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 2,477,265 | 0 | A | C | 29.1% | 83.5 / 14.4 | 55 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,741,871 | 0 | G | T | 24.5% | 301.1 / 15.1 | 143 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 4,296,304 | 0 | A | C | 24.3% | 56.8 / 11.5 | 37 | intergenic (+510/+132) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,054,886 | 0 | G | T | 24.1% | 174.0 / 12.3 | 87 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,623,537 | 0 | G | A | 22.9% | 213.3 / 17.7 | 127 | G47S (GGT→AGT) ‡ | yhhH | PF15631 family protein YhhH |
| * | NC_000913 | 3,623,538 | 0 | G | A | 20.5% | 217.9 / 16.5 | 127 | G47D (GGT→GAT) ‡ | yhhH | PF15631 family protein YhhH |
| * | NC_000913 | 2,818,324 | 0 | G | A | 20.0% | 86.6 / 12.8 | 40 | intergenic (‑50/+149) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4392437 | 61 (0.870) | 6 (0.120) | 5/434 | 3.4 | 9.9% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 64 (1.240) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 4094350 | 65 (0.930) | 6 (0.100) | 6/508 | 3.5 | 10.0% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 52 (0.860) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 2357730 | 81 (1.160) | 6 (0.100) | 6/510 | 3.5 | 8.5% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 60 (0.990) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1286906 | 25 (0.360) | 7 (0.110) | 7/550 | 3.5 | 22.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 25 (0.380) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1743492 | 0 (0.000) | 5 (0.070) | 5/584 | 4.2 | 100% | coding (36/1374 nt) | mdtK | multidrug efflux pump MdtK |
| ? | NC_000913 | = 2290114 | NA (NA) | pseudogene (67/67 nt) | yejO | adhesin‑like autotransporter YejO | |||||
| * | ? | NC_000913 | = 2904285 | 49 (0.700) | 4 (0.060) | 4/532 | 4.3 | 7.1% | intergenic (+911/+462) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| ? | NC_000913 | 2904408 = | 60 (0.950) | intergenic (+1034/+339) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE | |||||
| * | ? | NC_000913 | = 1287084 | 25 (0.360) | 4 (0.060) | 4/550 | 4.4 | 14.2% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 25 (0.380) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2281487 | 60 (0.860) | 4 (0.060) | 4/582 | 4.6 | 7.0% | coding (856/1761 nt) | radD | putative DNA repair helicase RadD |
| ? | NC_000913 | 2281969 = | 47 (0.680) | coding (1338/1761 nt) | radD | putative DNA repair helicase RadD | |||||
| * | ? | NC_000913 | = 2653419 | 54 (0.770) | 4 (0.060) | 3/540 | 4.8 | 6.9% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 59 (0.920) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 111492 | 62 (0.890) | 3 (0.050) | 3/552 | 4.8 | 4.7% | intergenic (+59/+157) | mutT/yacG | 8‑oxo‑dGTP diphosphatase/DNA gyrase inhibitor YacG |
| ? | NC_000913 | 111609 = | 64 (0.980) | intergenic (+176/+40) | mutT/yacG | 8‑oxo‑dGTP diphosphatase/DNA gyrase inhibitor YacG | |||||