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 56 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 3,895,018 | 0 | T | G | 33.9% | 70.4 / 11.5 | 64 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate transporter large permease YiaN |
| * | NC_007779 | 2,902,348 | 0 | C | A | 33.0% | 233.3 / 59.4 | 106 | intergenic (+318/+1055) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NC_007779 | 1,097,580 | 0 | C | T | 31.1% | 75.3 / 48.7 | 61 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 4,291,309 | 0 | T | A | 30.4% | 185.2 / 44.5 | 92 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 2,004,055 | 0 | A | C | 29.4% | 229.6 / 16.9 | 102 | intergenic (‑129/+192) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 658,098 | 0 | A | C | 27.6% | 193.9 / 22.7 | 88 | V88G (GTG→GGG) | crcB | fluoride efflux transporter CrcB |
| * | NC_007779 | 3,401,314 | 0 | T | C | 26.6% | 285.8 / 40.1 | 128 | D625G (GAT→GGT) | csrD | RNase E specificity factor CsrD |
| * | NC_007779 | 2,902,371 | 0 | G | A | 26.6% | 239.3 / 61.3 | 113 | intergenic (+341/+1032) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NC_007779 | 3,974,713 | 0 | G | T | 26.5% | 299.2 / 33.4 | 123 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NC_007779 | 4,609,024 | 0 | C | T | 25.7% | 211.1 / 25.2 | 101 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 1,437,441 | 0 | G | A | 25.3% | 190.9 / 36.8 | 83 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 2,004,048 | 0 | G | A | 25.0% | 208.9 / 38.2 | 100 | intergenic (‑122/+199) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 1,826,770 | 0 | G | A | 24.7% | 203.1 / 26.0 | 85 | intergenic (‑119/+84) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 1,097,540 | 0 | C | A | 24.6% | 148.5 / 25.0 | 57 | intergenic (+289/+85) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 2,902,367 | 0 | C | A | 24.6% | 355.9 / 39.0 | 114 | intergenic (+337/+1036) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NC_007779 | 29,496 | 0 | T | A | 24.5% | 368.3 / 50.6 | 143 | intergenic (+301/‑155) | dapB/Y75_RS00165 | 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit |
| * | NC_007779 | 1,515,709 | 0 | A | G | 24.2% | 205.3 / 25.0 | 100 | G55G (GGA→GGG) | Y75_RS07620 | ABC transporter permease |
| * | NC_007779 | 2,391,532 | 0 | G | A | 23.9% | 157.0 / 29.8 | 72 | intergenic (+31/‑72) | Y75_RS11940/Y75_RS11945 | M28 family peptidase/YfbM family protein |
| * | NC_007779 | 1,068,568 | 0 | T | G | 23.8% | 317.0 / 13.2 | 130 | G22G (GGT→GGG) | Y75_RS05245 | general stress protein |
| * | NC_007779 | 1,437,439 | 0 | C | A | 23.8% | 239.0 / 23.7 | 84 | intergenic (‑106/+35) | uspF/ompN | universal stress protein UspF/porin OmpN |
| 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) | 70 (0.490) | 61/492 | 4.3 | 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 | = 4547370 | 137 (0.960) | 57 (0.410) | 56/478 | 4.7 | 33.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 90 (0.650) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | 4547362 = | 134 (0.940) | 35 (0.250) | 33/478 | 9.5 | 24.0% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 93 (0.680) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 2946123 | 42 (0.290) | 5 (0.050) | 5/330 | 17.4 | 12.5% | intergenic (+4/‑30) | Y75_RS14670/Y75_RS14675 | tRNA‑Met/tRNA‑Met |
| ? | NC_007779 | 2946344 = | 42 (0.440) | intergenic (+5/+69) | Y75_RS14680/Y75_RS14685 | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC | |||||
| * | ? | NC_007779 | 1413613 = | 151 (1.060) | 7 (0.050) | 7/444 | 19.8 | 4.9% | coding (50/936 nt) | ttcA | tRNA 2‑thiocytidine(32) synthetase TtcA |
| ? | NC_007779 | = 1436672 | 135 (1.060) | intergenic (+39/+227) | Y75_RS24865/uspF | hypothetical protein/universal stress protein UspF | |||||
| * | ? | NC_007779 | 3541999 = | 125 (0.880) | 12 (0.090) +23 bp |
5/450 | 21.6 | 8.9% | intergenic (+41/‑410) | rhaA/rhaD | L‑rhamnose isomerase/rhamnulose‑1‑phosphate aldolase |
| ? | NC_007779 | = 3542343 | 145 (1.020) | intergenic (+385/‑66) | rhaA/rhaD | L‑rhamnose isomerase/rhamnulose‑1‑phosphate aldolase | |||||