mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
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 | 4,307,290 | 0 | T | C | 28.6% | 26.8 / 11.4 | 21 | G170G (GGA→GGG) | alsK | D‑allose kinase |
| * | NC_000913 | 4,307,294 | 0 | A | T | 28.6% | 29.5 / 12.7 | 21 | L169Q (CTG→CAG) | alsK | D‑allose kinase |
| * | NC_000913 | 4,307,298 | 0 | G | A | 28.6% | 27.5 / 11.0 | 21 | P168S (CCC→TCC) | alsK | D‑allose kinase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.4% | 71.3 / 21.1 | 41 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,807,318 | 0 | A | G | 21.6% | 68.6 / 15.7 | 37 | intergenic (+19/‑82) | pfkB/ydiZ | 6‑phosphofructokinase II/uncharacterized protein |
| * | NC_000913 | 2,637,235 | 0 | T | G | 21.4% | 51.1 / 12.9 | 28 | K41T (AAG→ACG) | der | GTPase; multicopy suppressor of ftsJ |
| * | NC_000913 | 1,807,316 | 0 | G | A | 21.1% | 75.6 / 13.8 | 38 | intergenic (+17/‑84) | pfkB/ydiZ | 6‑phosphofructokinase II/uncharacterized protein |
| * | NC_000913 | 1,807,317 | 0 | C | T | 21.1% | 73.1 / 14.9 | 38 | intergenic (+18/‑83) | pfkB/ydiZ | 6‑phosphofructokinase II/uncharacterized protein |
| * | NC_000913 | 1,807,319 | 0 | T | C | 21.1% | 71.5 / 16.2 | 38 | intergenic (+20/‑81) | pfkB/ydiZ | 6‑phosphofructokinase II/uncharacterized protein |
| * | NC_000913 | 3,891,502 | 0 | C | G | 20.7% | 64.9 / 14.3 | 29 | intergenic (+19/‑113) | tnaB/mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| * | NC_000913 | 3,923,718 | 0 | G | C | 20.7% | 64.8 / 13.1 | 29 | intergenic (‑38/+26) | rsmG/mnmG | 16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein/5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| * | NC_000913 | 3,923,719 | 0 | G | C | 20.7% | 64.4 / 13.2 | 29 | intergenic (‑39/+25) | rsmG/mnmG | 16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein/5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| * | NC_000913 | 4,041,216 | 0 | T | C | 20.5% | 75.6 / 15.6 | 39 | Q73R (CAG→CGG) | mobB | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| * | NC_000913 | 4,041,217 | 0 | G | A | 20.5% | 78.4 / 15.1 | 39 | Q73* (CAG→TAG) | mobB | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| * | NC_000913 | 4,041,220 | 0 | T | C | 20.5% | 76.1 / 15.6 | 39 | S72G (AGC→GGC) | mobB | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| * | NC_000913 | 4,041,221 | 0 | G | A | 20.5% | 78.4 / 15.5 | 39 | A71A (GCC→GCT) | mobB | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| * | NC_000913 | 2,302,452 | 0 | A | C | 20.0% | 70.5 / 11.1 | 35 | L101R (CTG→CGG) | napA | nitrate reductase, periplasmic, large subunit |
| * | NC_000913 | 2,960,928 | 0 | C | G | 20.0% | 73.3 / 11.8 | 30 | G501R (GGC→CGC) | recC | exonuclease V (RecBCD complex), gamma chain |
| * | NC_000913 | 3,891,504 | 0 | T | A | 20.0% | 64.0 / 11.7 | 30 | intergenic (+21/‑111) | tnaB/mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| * | NC_000913 | 3,891,506 | 0 | C | G | 20.0% | 75.3 / 11.7 | 31 | intergenic (+23/‑109) | tnaB/mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| Marginal new junction evidence (lowest skew 10 of 53 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 114505 | 31 (0.910) | 6 (0.200) | 6/220 | 3.0 | 16.9% | intergenic (+18/+17) | guaC/hofC | GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein |
| ? | NC_000913 | = 114511 | 31 (1.010) | intergenic (+24/+11) | guaC/hofC | GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 7 (0.220) | 6/226 | 3.1 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 250165 = | 32 (0.940) | 7 (0.220) | 6/230 | 3.1 | 18.4% | pseudogene (94/756 nt) | lafU | pseudogene, lateral flagellar motor protein fragment |
| ? | NC_000913 | 250214 = | 32 (1.000) | pseudogene (143/756 nt) | lafU | pseudogene, lateral flagellar motor protein fragment | |||||
| * | ? | NC_000913 | 66735 = | 74 (2.180) | 6 (0.190) | 6/230 | 3.1 | 8.5% | noncoding (171/248 nt) | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences |
| ? | NC_000913 | 66760 = | 60 (1.870) | noncoding (196/248 nt) | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | |||||
| * | ? | NC_000913 | 66650 = | 41 (1.210) | 6 (0.190) | 6/230 | 3.1 | 10.8% | noncoding (86/248 nt) | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences |
| ? | NC_000913 | 66760 = | 60 (1.870) | noncoding (196/248 nt) | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | |||||
| * | ? | NC_000913 | 66565 = | NA (NA) | 6 (0.190) | 6/230 | 3.1 | 9.1% | noncoding (1/248 nt) | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences |
| ? | NC_000913 | 66760 = | 60 (1.870) | noncoding (196/248 nt) | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | REP6 (repetitive extragenic palindromic) element; contains 6 REP sequences | |||||
| * | ? | NC_000913 | = 4040683 | 27 (0.790) | 15 (0.450) | 6/240 | 3.3 | 34.7% | intergenic (+47/+223) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913 | = 4213162 | 30 (0.900) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913 | 2077179 = | 36 (1.060) | 6 (0.190) | 5/228 | 3.4 | 14.5% | coding (68/369 nt) | cbeA | CP4‑44 prophage; cytoskeleton bundling‑enhancing factor A; CbtA antitoxin |
| ? | NC_000913 | 2077221 = | 37 (1.170) | coding (110/369 nt) | cbeA | CP4‑44 prophage; cytoskeleton bundling‑enhancing factor A; CbtA antitoxin | |||||
| * | ? | NC_000913 | 1849289 = | 21 (0.620) | 5 (0.160) | 5/228 | 3.4 | 21.9% | coding (453/1857 nt) | sppA | protease IV (signal peptide peptidase) |
| ? | NC_000913 | 1849327 = | 16 (0.500) | coding (491/1857 nt) | sppA | protease IV (signal peptide peptidase) | |||||
| * | ? | NC_000913 | = 3360642 | 32 (0.940) | 4 (0.130) | 4/222 | 3.7 | 12.7% | intergenic (+26/‑534) | gltD/gltF | glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein |
| ? | NC_000913 | = 3360645 | 26 (0.840) | intergenic (+29/‑531) | gltD/gltF | glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein | |||||