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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,922,815 | 0 | C | A | 39.1% | 88.3 / 28.7 | 87 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 1,375,723 | 0 | C | A | 36.9% | 104.4 / 17.4 | 84 | S254Y (TCC→TAC) | ycjQ | D‑guloside 3‑dehydrogenase |
| * | NC_000913 | 3,054,886 | 0 | G | T | 34.1% | 135.7 / 30.2 | 86 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.1% | 158.5 / 25.3 | 88 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,073,613 | 0 | G | T | 33.3% | 129.9 / 11.7 | 72 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 2,159,413 | 0 | C | T | 32.6% | 66.1 / 12.2 | 46 | A343V (GCG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 967,676 | 0 | G | T | 32.4% | 105.4 / 12.0 | 71 | P352P (CCG→CCT) | msbA | ATP‑binding lipopolysaccharide transport protein |
| * | NC_000913 | 1,756,353 | 0 | C | A | 30.6% | 159.0 / 10.3 | 85 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| * | NC_000913 | 1,097,118 | 0 | C | A | 30.3% | 42.3 / 12.8 | 33 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,767,445 | 0 | C | A | 30.2% | 187.3 / 22.8 | 99 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 161,549 | 0 | A | C | 29.8% | 112.8 / 10.6 | 67 | R161R (CGT→CGG) | thpR | RNA 2',3'‑cyclic phosphodiesterase |
| * | NC_000913 | 2,159,415 | 0 | C | G | 29.7% | 83.9 / 12.1 | 46 | L344V (CTG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 58,065 | 0 | C | A | 29.7% | 190.3 / 10.9 | 101 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,502,770 | 0 | T | C | 29.1% | 127.9 / 24.2 | 79 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 1,390,607 | 0 | C | A | 29.0% | 154.3 / 13.7 | 107 | intergenic (‑9/+73) | mpaA/ymjC | murein tripeptide amidase A/putative uncharacterized protein YmjC |
| * | NC_000913 | 2,767,443 | 0 | C | A | 28.9% | 205.3 / 11.7 | 99 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,911,533 | 0 | C | A | 28.2% | 274.1 / 15.4 | 149 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,543,220 | 0 | A | C | 28.1% | 253.6 / 15.7 | 121 | L18F (TTA→TTC) | rpnA | recombination‑promoting nuclease RpnA |
| * | NC_000913 | 2,013,023 | 0 | C | A | 27.5% | 141.0 / 11.3 | 91 | intergenic (‑9/‑206) | fliE/fliF | flagellar protein FliE/flagellar basal‑body MS‑ring and collar protein |
| * | NC_000913 | 1,902,613 | 0 | C | A | 27.4% | 229.2 / 19.9 | 113 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| 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 | 382179 = | NA (NA) | 25 (0.260) | 21/594 | 3.4 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 4542690 | 135 (1.410) | 17 (0.180) | 15/580 | 4.5 | 12.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 103 (1.110) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 131 (1.360) | 17 (0.180) | 15/580 | 4.5 | 12.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 103 (1.110) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4606166 | 112 (1.170) | 4 (0.060) | 4/420 | 6.8 | 4.7% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 82 (1.220) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781322 | 64 (0.670) | 8 (0.100) | 6/520 | 6.9 | 12.4% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 57 (0.680) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 1287329 | 64 (0.670) | 3 (0.040) | 3/424 | 7.4 | 6.8% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 37 (0.540) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 45574 | 97 (1.010) | 6 (0.060) | 6/576 | 7.4 | 6.2% | coding (112/288 nt) | fixX | putative ferredoxin FixX |
| ? | NC_000913 | 45934 = | 89 (0.960) | coding (128/1332 nt) | yaaU | putative transporter YaaU | |||||
| * | ? | NC_000913 | = 696506 | 92 (0.960) | 3 (0.040) | 3/444 | 7.7 | 4.6% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 696619 = | 57 (0.800) | intergenic (‑3/+45) | glnV/metU | tRNA‑Gln/tRNA‑Met | |||||
| * | ? | NC_000913 | = 2653502 | 108 (1.130) | 4 (0.050) | 4/530 | 8.0 | 4.4% | intergenic (‑47/‑353) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| ? | NC_000913 | 2653825 = | 78 (0.920) | intergenic (‑370/‑30) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2653419 | 92 (0.960) | 4 (0.050) | 4/548 | 8.2 | 4.8% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 76 (0.860) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||