mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_bme_pgi | 4,158,779 | 0 | T | G | 64.5% | 26.4 / 31.9 | 31 | L97W (TTG→TGG) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_bme_pgi | 1,756,497 | 0 | G | T | 63.6% | 30.2 / 34.4 | 33 | C267F (TGT→TTT) | pykF | pyruvate kinase I |
| * | NC_000913_3_bme_pgi | 4,158,885 | 0 | A | C | 63.6% | 33.8 / 33.8 | 33 | L132F (TTA→TTC) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_bme_pgi | 3,546,391 | 0 | C | T | 53.8% | 6.9 / 45.7 | 39 | intergenic (+192/‑168) | nfuA/gntT | Fe/S biogenesis protein, putative scaffold/chaperone protein/gluconate transporter, high‑affinity GNT I system |
| * | NC_000913_3_bme_pgi | 1,233,157 | 0 | T | A | 38.9% | 11.7 / 20.2 | 18 | intergenic (‑127/+19) | dsbB/nhaB | oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter |
| * | NC_000913_3_bme_pgi | 1,233,154 | 0 | T | A | 36.8% | 15.6 / 19.9 | 19 | intergenic (‑124/+22) | dsbB/nhaB | oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter |
| * | NC_000913_3_bme_pgi | 2,074,691 | 0 | C | G | 31.6% | 55.1 / 38.0 | 38 | intergenic (+33/‑88) | flu/yeeR | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein |
| * | NC_000913_3_bme_pgi | 4,262,256 | 0 | G | C | 30.3% | 49.6 / 30.4 | 34 | S196T (AGC→ACC) | dusA | tRNA‑dihydrouridine synthase A |
| * | NC_000913_3_bme_pgi | 4,262,251 | 0 | G | C | 29.4% | 45.7 / 29.8 | 34 | G194G (GGG→GGC) | dusA | tRNA‑dihydrouridine synthase A |
| * | NC_000913_3_bme_pgi | 4,296,061 | 0 | C | T | 25.0% | 77.1 / 29.0 | 49 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_bme_pgi | 639,724 | 0 | T | G | 23.1% | 66.4 / 26.9 | 39 | intergenic (+216/‑29) | ahpC/ahpF | alkyl hydroperoxide reductase, C22 subunit/alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| * | NC_000913_3_bme_pgi | 1,449,050 | 0 | T | A | 23.1% | 108.8 / 35.2 | 52 | intergenic (+32/+26) | feaB/tynA | phenylacetaldehyde dehydrogenase/tyramine oxidase, copper‑requiring |
| * | NC_000913_3_bme_pgi | 2,866,487 | 0 | G | C | 22.9% | 74.1 / 20.8 | 35 | intergenic (+22/+72) | ygbN/rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| * | NC_000913_3_bme_pgi | 2,866,488 | 0 | G | C | 22.9% | 74.7 / 19.9 | 35 | intergenic (+23/+71) | ygbN/rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| * | NC_000913_3_bme_pgi | 3,891,502 | 0 | C | G | 22.2% | 80.3 / 22.8 | 36 | intergenic (+19/‑113) | tnaB/mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| * | NC_000913_3_bme_pgi | 4,088,091 | 0 | G | C | 22.2% | 81.1 / 22.4 | 36 | intergenic (+34/+16) | yiiG/frvR | DUF3829 family lipoprotein/putative frv operon regulator; contains a PTS EIIA domain |
| * | NC_000913_3_bme_pgi | 2,305,085 | 0 | A | G | 21.9% | 86.1 / 17.8 | 41 | intergenic (+692/+23) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913_3_bme_pgi | 2,305,086 | 0 | C | G | 21.9% | 102.8 / 25.5 | 41 | intergenic (+693/+22) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913_3_bme_pgi | 2,305,087 | 0 | C | T | 21.9% | 83.7 / 18.8 | 41 | intergenic (+694/+21) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913_3_bme_pgi | 22,773 | 0 | A | T | 21.7% | 49.9 / 11.0 | 23 | E128V (GAA→GTA) | ileS | isoleucyl‑tRNA synthetase |
| Marginal new junction evidence (lowest skew 10 of 213 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_bme_pgi | 4233518 = | 643 (17.360) | 30 (0.930) | 22/212 | 0.6 | 5.1% | intergenic (‑285/‑2389) | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| ? | NC_000913_3_bme_pgi | 4233534 = | 555 (17.240) | intergenic (‑301/‑2373) | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein | |||||
| * | ? | NC_000913_3_bme_pgi | 4227808 = | 648 (17.490) | 34 (0.960) | 22/234 | 0.7 | 5.1% | coding (78/1632 nt) | yjbB | putative Na+/Pi‑cotransporter |
| ? | NC_000913_3_bme_pgi | 4227825 = | 645 (18.160) | coding (95/1632 nt) | yjbB | putative Na+/Pi‑cotransporter | |||||
| * | ? | NC_000913_3_bme_pgi | = 4229386 | 661 (17.840) | 28 (0.800) | 20/230 | 0.9 | 4.3% | noncoding (11/70 nt) | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_bme_pgi | = 4229405 | NA (NA) | noncoding (30/70 nt) | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | 4226588 = | 554 (14.960) | 20 (0.540) | 19/242 | 1.1 | 3.6% | coding (2761/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| ? | NC_000913_3_bme_pgi | 4226623 = | 521 (14.180) | coding (2796/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent | |||||
| * | ? | NC_000913_3_bme_pgi | = 4227812 | 648 (17.490) | 20 (0.560) | 14/234 | 1.7 | 3.1% | coding (82/1632 nt) | yjbB | putative Na+/Pi‑cotransporter |
| ? | NC_000913_3_bme_pgi | = 4227819 | 645 (18.160) | coding (89/1632 nt) | yjbB | putative Na+/Pi‑cotransporter | |||||
| * | ? | NC_000913_3_bme_pgi | = 4235432 | 466 (12.580) | 16 (0.460) | 13/230 | 1.8 | 3.5% | noncoding (11/77 nt) | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_bme_pgi | = 4235448 | NA (NA) | noncoding (27/77 nt) | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | = 4226475 | 528 (14.250) | 20 (0.570) | 13/232 | 1.8 | 3.8% | coding (2648/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| ? | NC_000913_3_bme_pgi | = 4226484 | 511 (14.510) | coding (2657/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent | |||||
| * | ? | NC_000913_3_bme_pgi | 4226590 = | 551 (14.870) | 13 (0.370) | 12/230 | 2.0 | 2.5% | coding (2763/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| ? | NC_000913_3_bme_pgi | 4226621 = | 514 (14.720) | coding (2794/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent | |||||
| * | ? | NC_000913_3_bme_pgi | 4235057 = | 580 (15.660) | 16 (0.460) | 11/230 | 2.2 | 2.9% | intergenic (‑1824/‑850) | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| ? | NC_000913_3_bme_pgi | 4235081 = | 526 (15.060) | intergenic (‑1848/‑826) | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein | |||||
| * | ? | NC_000913_3_bme_pgi | 4226470 = | 528 (14.250) | 13 (0.370) | 11/232 | 2.2 | 2.5% | coding (2643/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| ? | NC_000913_3_bme_pgi | 4226491 = | 511 (14.510) | coding (2664/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent | |||||