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 (highest frequency 20 of 42 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.6% | 214.8 / 20.2 | 136 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 4,296,191 | 0 | A | C | 34.5% | 23.7 / 14.2 | 29 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 58,065 | 0 | C | A | 32.6% | 152.6 / 20.2 | 98 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 2,767,445 | 0 | C | A | 32.6% | 201.1 / 16.0 | 97 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,955,561 | 0 | C | A | 32.0% | 119.7 / 12.2 | 75 | E483* (GAG→TAG) | torZ | trimethylamine N‑oxide reductase 2 |
| * | NC_000913 | 1,502,772 | 0 | G | A | 31.3% | 151.2 / 26.7 | 100 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 2,047,219 | 0 | C | A | 31.2% | 233.1 / 20.1 | 128 | S761* (TCG→TAG) | yeeJ | inverse autotransporter adhesin |
| * | NC_000913 | 2,767,443 | 0 | C | A | 31.2% | 209.9 / 12.1 | 97 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,856,087 | 0 | G | T | 30.9% | 129.3 / 15.5 | 97 | E584* (GAG→TAG) | fhlA | DNA‑binding transcriptional activator FhlA |
| * | NC_000913 | 3,791,179 | 0 | G | T | 30.4% | 201.4 / 11.7 | 116 | P56Q (CCG→CAG) | tdh | threonine dehydrogenase |
| * | NC_000913 | 141,849 | 0 | C | A | 30.4% | 196.3 / 25.0 | 112 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 4,360,965 | 0 | C | A | 29.2% | 296.1 / 17.1 | 147 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 1,812,509 | 0 | G | T | 29.2% | 211.0 / 12.0 | 114 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 1,502,770 | 0 | T | C | 29.0% | 164.7 / 33.8 | 100 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 3,741,871 | 0 | G | T | 28.2% | 211.2 / 14.8 | 103 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 1,351,463 | 0 | C | A | 27.2% | 133.4 / 10.3 | 81 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 2,767,444 | 0 | C | A | 27.1% | 217.3 / 11.0 | 97 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 564,850 | 0 | G | T | 26.6% | 186.8 / 13.5 | 94 | H377N (CAC→AAC) | intD | putative integrase |
| * | NC_000913 | 3,469,862 | 0 | C | A | 26.6% | 186.8 / 12.5 | 113 | intergenic (‑9/+283) | chiA/tufA | endochitinase/translation elongation factor Tu 1 |
| * | NC_000913 | 1,015,488 | 0 | C | A | 26.2% | 252.6 / 11.1 | 130 | intergenic (+29/‑227) | pqiC/rmf | intermembrane transport lipoprotein PqiC/ribosome modulation factor |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 117 (1.270) | 20 (0.220) | 17/568 | 3.6 | 16.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 85 (0.960) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 109 (1.190) | 21 (0.240) | 15/568 | 4.1 | 17.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 87 (0.980) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3992343 | 68 (0.740) | 17 (0.190) | 14/586 | 4.5 | 20.6% | coding (1191/2547 nt) | cyaA | adenylate cyclase |
| ? | NC_000913 | 3992359 = | 63 (0.690) | coding (1207/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | 2818197 = | 55 (0.600) | 10 (0.150) | 8/428 | 4.7 | 16.5% | intergenic (‑62/+1) | argZ/argY | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | = 2818471 | 61 (0.910) | intergenic (‑197/+2) | argY/argV | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | = 781222 | 70 (0.760) | 8 (0.120) | 6/434 | 5.6 | 14.4% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 43 (0.630) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4606166 | 85 (0.930) | 5 (0.080) | 5/408 | 5.8 | 6.9% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 75 (1.170) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 1286906 | 67 (0.730) | 8 (0.090) | 7/546 | 6.3 | 12.8% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 47 (0.550) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2357730 | 124 (1.350) | 6 (0.080) | 6/506 | 6.4 | 5.5% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 99 (1.250) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1166125 | 93 (1.010) | 7 (0.080) | 7/556 | 6.4 | 8.2% | coding (41/1305 nt) | ndh | NADH:quinone oxidoreductase II |
| ? | NC_000913 | 1166621 = | 68 (0.780) | coding (537/1305 nt) | ndh | NADH:quinone oxidoreductase II | |||||
| * | ? | NC_000913 | = 2518116 | 74 (0.810) | 4 (0.060) | 4/424 | 6.5 | 7.0% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 53 (0.800) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||