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 57 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 1,097,580 | 0 | C | T | 34.7% | 134.1 / 124.2 | 124 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 432,858 | 0 | T | G | 31.3% | 244.1 / 29.3 | 150 | G60G (GGT→GGG) | ribD | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase RibD |
| * | NC_007779 | 4,609,024 | 0 | C | T | 30.6% | 263.1 / 67.1 | 147 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 1,437,441 | 0 | G | A | 29.8% | 375.1 / 75.8 | 171 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 3,205,091 | 0 | C | T | 29.7% | 251.0 / 66.4 | 145 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 2,004,055 | 0 | A | C | 29.5% | 407.4 / 29.3 | 173 | intergenic (‑129/+192) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 3,205,102 | 0 | C | A | 29.0% | 251.7 / 44.6 | 148 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 2,488,700 | 0 | G | A | 28.1% | 393.8 / 56.1 | 178 | S29L (TCA→TTA) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 2,902,348 | 0 | C | A | 27.5% | 526.9 / 84.1 | 193 | intergenic (+318/+1055) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NC_007779 | 4,291,309 | 0 | T | A | 27.2% | 383.6 / 82.8 | 173 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 29,496 | 0 | T | A | 25.4% | 436.9 / 63.9 | 173 | intergenic (+301/‑155) | dapB/Y75_RS00165 | 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit |
| * | NC_007779 | 2,004,048 | 0 | G | A | 24.9% | 376.9 / 61.9 | 169 | intergenic (‑122/+199) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 1,097,540 | 0 | C | A | 24.8% | 319.7 / 56.3 | 117 | intergenic (+289/+85) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 3,974,713 | 0 | G | T | 24.6% | 544.4 / 68.0 | 197 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NC_007779 | 4,609,030 | 0 | C | T | 24.3% | 305.0 / 39.5 | 136 | S64F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 1,555,714 | 0 | T | G | 24.1% | 221.8 / 16.1 | 109 | Y557S (TAC→TCC) | Y75_RS07805 | NAD‑dependent malic enzyme |
| * | NC_007779 | 634,289 | 0 | C | A | 23.9% | 482.7 / 41.5 | 167 | G104V (GGT→GTT) | Y75_RS03120 | ParB‑like nuclease domain‑containing protein |
| * | NC_007779 | 2,188,533 | 0 | T | G | 23.9% | 361.2 / 33.4 | 159 | T35P (ACC→CCC) | thiM | hydroxyethylthiazole kinase |
| * | NC_007779 | 4,291,306 | 0 | C | A | 23.4% | 471.2 / 43.0 | 175 | intergenic (‑345/‑48) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 1,826,775 | 0 | G | A | 23.4% | 370.2 / 38.0 | 141 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 381401 = | NA (NA) | 143 (0.650) | 115/492 | 3.1 | NA | coding (512/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 381812 | NA (NA) | pseudogene (174/174 nt) | Y75_RS23175 | acetyltransferase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 119 (0.540) | 94/496 | 5.6 | 96.8% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 4 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 4547370 | 254 (1.150) | 24 (0.110) | 24/478 | 23.1 | 8.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 245 (1.150) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | 4547362 = | 255 (1.150) | 22 (0.100) | 22/478 | 24.0 | 8.2% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 245 (1.150) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 2069490 | 263 (1.190) | 119 (0.540) | 19/496 | 26.3 | 47.1% | intergenic (‑32/+1) | Y75_RS10470/Y75_RS24935 | IS5‑like element IS5 family transposase/hypothetical protein |
| ? | NC_007779 | = 4540919 | 4 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 1097400 = | 163 (0.740) | 33 (0.150) +G |
17/494 | 27.4 | 19.7% | intergenic (+149/+225) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| ? | NC_007779 | = 1097760 | 108 (0.490) | noncoding (2/137 nt) | Y75_RS05385 | RtT sRNA | |||||
| * | ? | NC_007779 | 4299422 = | 196 (0.880) | 3 (0.020) | 3/418 | 35.0 | 1.8% | intergenic (+38/+493) | gltP/Y75_RS21270 | glutamate/aspartate:proton symporter GltP/sel1 repeat family protein |
| ? | NC_007779 | = 4299873 | 164 (0.880) | intergenic (+489/+42) | gltP/Y75_RS21270 | glutamate/aspartate:proton symporter GltP/sel1 repeat family protein | |||||
| * | ? | NC_007779 | 967452 = | 207 (0.930) | 3 (0.010) | 3/476 | 37.6 | 1.5% | coding (410/1749 nt) | msbA | lipid A ABC transporter ATP‑binding protein/permease MsbA |
| ? | NC_007779 | = 967448 | 196 (0.920) | coding (406/1749 nt) | msbA | lipid A ABC transporter ATP‑binding protein/permease MsbA | |||||
| * | ? | NC_007779 | 614186 = | 236 (1.060) | 3 (0.010) | 3/480 | 37.8 | 1.3% | coding (807/3882 nt) | entF | enterobactin non‑ribosomal peptide synthetase EntF |
| ? | NC_007779 | 614229 = | 226 (1.050) | coding (850/3882 nt) | entF | enterobactin non‑ribosomal peptide synthetase EntF | |||||
| * | ? | NC_007779 | 3837650 = | 251 (1.130) | 3 (0.010) | 3/492 | 38.3 | 1.2% | coding (294/1020 nt) | waaO | lipopolysaccharide 3‑alpha‑galactosyltransferase |
| ? | NC_007779 | 3837669 = | 252 (1.150) | coding (313/1020 nt) | waaO | lipopolysaccharide 3‑alpha‑galactosyltransferase | |||||