mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 37.0% | 26.8 / 23.3 | 27 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 3,959,515 | 0 | T | A | 33.3% | 26.4 / 21.3 | 27 | intergenic (+70/+17) | ilvC/ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| * | NC_000913 | 1,912,748 | 0 | T | G | 29.2% | 31.7 / 14.6 | 24 | intergenic (‑172/+20) | htpX/prc | putative endopeptidase/carboxy‑terminal protease for penicillin‑binding protein 3 |
| * | NC_000913 | 1,912,749 | 0 | T | A | 29.2% | 30.9 / 15.4 | 24 | intergenic (‑173/+19) | htpX/prc | putative endopeptidase/carboxy‑terminal protease for penicillin‑binding protein 3 |
| * | NC_000913 | 1,912,750 | 0 | T | A | 29.2% | 32.2 / 15.6 | 24 | intergenic (‑174/+18) | htpX/prc | putative endopeptidase/carboxy‑terminal protease for penicillin‑binding protein 3 |
| * | NC_000913 | 1,388,284 | 0 | A | T | 28.9% | 52.0 / 25.6 | 39 | intergenic (+23/+21) | tyrR/tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| * | NC_000913 | 1,912,751 | 0 | C | A | 26.9% | 42.9 / 16.2 | 26 | intergenic (‑175/+17) | htpX/prc | putative endopeptidase/carboxy‑terminal protease for penicillin‑binding protein 3 |
| * | NC_000913 | 1,388,283 | 0 | C | T | 25.6% | 64.8 / 20.4 | 39 | intergenic (+22/+22) | tyrR/tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| * | NC_000913 | 1,388,285 | 0 | A | G | 25.6% | 59.1 / 21.9 | 39 | intergenic (+24/+20) | tyrR/tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| * | NC_000913 | 2,121,588 | 1 | . | C | 24.1% | 60.0 / 28.6 | 29 | intergenic (‑34/+21) | wcaJ/cpsG | colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase |
| * | NC_000913 | 2,657,426 | 0 | G | A | 23.1% | 46.0 / 10.4 | 26 | L504L (CTG→TTG) | hscA | DnaK‑like molecular chaperone specific for IscU |
| * | NC_000913 | 2,121,583 | 0 | G | . | 22.6% | 78.8 / 20.8 | 31 | intergenic (‑29/+26) | wcaJ/cpsG | colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase |
| * | NC_000913 | 2,121,586 | 0 | G | C | 22.6% | 63.0 / 18.0 | 31 | intergenic (‑32/+23) | wcaJ/cpsG | colanic biosynthesis UDP‑glucose lipid carrier transferase/phosphomannomutase |
| * | NC_000913 | 3,891,502 | 0 | C | G | 21.6% | 72.4 / 20.9 | 37 | intergenic (+19/‑113) | tnaB/mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| * | NC_000913 | 3,368,219 | 0 | G | A | 21.4% | 52.3 / 10.2 | 28 | T131T (ACG→ACA) | yhcG | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| * | NC_000913 | 3,368,220 | 0 | C | G | 21.4% | 60.4 / 14.8 | 28 | L132V (CTG→GTG) | yhcG | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| * | NC_000913 | 2,657,432 | 0 | A | C | 20.7% | 52.7 / 14.2 | 29 | Y502D (TAC→GAC) | hscA | DnaK‑like molecular chaperone specific for IscU |
| * | NC_000913 | 2,657,433 | 0 | A | T | 20.7% | 50.0 / 11.5 | 29 | S501S (TCT→TCA) | hscA | DnaK‑like molecular chaperone specific for IscU |
| * | NC_000913 | 2,657,434 | 0 | G | T | 20.7% | 69.0 / 11.9 | 29 | S501Y (TCT→TAT) | hscA | DnaK‑like molecular chaperone specific for IscU |
| * | NC_000913 | 3,368,221 | 0 | T | C | 20.7% | 54.8 / 10.1 | 29 | L132P (CTG→CCG) | yhcG | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| Marginal new junction evidence (lowest skew 10 of 40 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 684883 | 26 (0.840) | 6 (0.200) | 5/252 | 3.2 | 19.2% | coding (373/726 nt) | gltL | glutamate/aspartate ABC transporter ATPase |
| ? | NC_000913 | = 684903 | 26 (0.880) | coding (353/726 nt) | gltL | glutamate/aspartate ABC transporter ATPase | |||||
| * | ? | NC_000913 | = 4341795 | 37 (1.190) | 4 (0.150) | 4/230 | 3.3 | 10.7% | intergenic (‑167/‑116) | melR/melA | melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding |
| ? | NC_000913 | = 4341815 | 35 (1.310) | intergenic (‑187/‑96) | melR/melA | melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding | |||||
| * | ? | NC_000913 | = 4610792 | 26 (0.840) | 4 (0.140) | 4/248 | 3.5 | 16.9% | coding (1379/1590 nt) | prfC | peptide chain release factor RF‑3 |
| ? | NC_000913 | = 4610809 | 15 (0.520) | coding (1396/1590 nt) | prfC | peptide chain release factor RF‑3 | |||||
| * | ? | NC_000913 | = 4241701 | 37 (1.190) | 4 (0.140) | 4/252 | 3.5 | 9.9% | coding (554/1476 nt) | xylE | D‑xylose transporter |
| ? | NC_000913 | = 4241729 | 38 (1.290) | coding (526/1476 nt) | xylE | D‑xylose transporter | |||||
| * | ? | NC_000913 | = 3973018 | 37 (1.190) | 4 (0.130) | 4/254 | 3.5 | 11.5% | coding (497/1068 nt) | rffG | dTDP‑glucose 4,6‑dehydratase |
| ? | NC_000913 | = 3973039 | 26 (0.880) | coding (518/1068 nt) | rffG | dTDP‑glucose 4,6‑dehydratase | |||||
| * | ? | NC_000913 | = 3783805 | 31 (1.000) | 4 (0.140) | 4/250 | 3.5 | 10.7% | coding (324/468 nt) | secB | protein export chaperone |
| ? | NC_000913 | = 3783825 | 38 (1.300) | coding (304/468 nt) | secB | protein export chaperone | |||||
| * | ? | NC_000913 | 3235543 = | 28 (0.900) | 4 (0.140) | 4/252 | 3.5 | 13.0% | coding (333/1137 nt) | rlmG | 23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| ? | NC_000913 | 3235583 = | 27 (0.920) | coding (293/1137 nt) | rlmG | 23S rRNA m(2)G1835 methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 3134555 | 37 (1.190) | 6 (0.200) | 4/254 | 3.5 | 13.4% | coding (425/693 nt) | yghT | putative ATP‑binding protein |
| ? | NC_000913 | = 3134592 | 42 (1.420) | coding (462/693 nt) | yghT | putative ATP‑binding protein | |||||
| * | ? | NC_000913 | 1510110 = | 37 (1.190) | 5 (0.170) | 4/252 | 3.5 | 13.0% | coding (108/1407 nt) | ydcR | putative DNA‑binding transcriptional regulator and putative aminotransferase |
| ? | NC_000913 | 1510142 = | 32 (1.090) | coding (140/1407 nt) | ydcR | putative DNA‑binding transcriptional regulator and putative aminotransferase | |||||
| * | ? | NC_000913 | 1179565 = | 15 (0.480) | 4 (0.130) | 4/254 | 3.5 | 21.4% | intergenic (+61/‑66) | nagK/cobB | N‑acetyl‑D‑glucosamine kinase/deacetylase of acs and cheY, chemotaxis regulator |
| ? | NC_000913 | 1179588 = | 15 (0.510) | intergenic (+84/‑43) | nagK/cobB | N‑acetyl‑D‑glucosamine kinase/deacetylase of acs and cheY, chemotaxis regulator | |||||