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 35 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,980,951 | 1 | . | G | 74.5% | 297.0 / 106.4 | 102 | coding (65/1386 nt) | yifK | putative transporter YifK |
| * | NC_000913 | 214,885 | 0 | C | T | 74.0% | 192.0 / 73.9 | 100 | T18I (ACC→ATC) | arfB | peptidyl‑tRNA hydrolase, ribosome rescue factor |
| * | NC_000913 | 366,351 | 0 | A | T | 72.5% | 363.6 / 152.8 | 178 | intergenic (‑46/+77) | lacZ/lacI | beta‑galactosidase/DNA‑binding transcriptional repressor LacI |
| * | NC_000913 | 366,352 | 0 | C | T | 72.5% | 340.6 / 134.2 | 178 | intergenic (‑47/+76) | lacZ/lacI | beta‑galactosidase/DNA‑binding transcriptional repressor LacI |
| * | NC_000913 | 1,811,208 | 0 | T | C | 72.4% | 258.5 / 129.4 | 152 | V92A (GTT→GCT) | tcyP | cystine/sulfocysteine:cation symporter |
| * | NC_000913 | 3,816,579 | 0 | G | A | 71.5% | 261.1 / 126.3 | 151 | intergenic (‑30/‑97) | rph/yicC | truncated RNase PH/UPF0701 family protein YicC |
| * | NC_000913 | 388,654 | 0 | G | . | 53.3% | 22.0 / 35.5 | 15 | intergenic (+8/+99) | tauD/hemB | taurine dioxygenase/porphobilinogen synthase |
| * | NC_000913 | 1,562,085 | 0 | C | T | 37.5% | 116.5 / 145.2 | 120 | A133T (GCA→ACA) | ddpA | putative D,D‑dipeptide ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,875,050 | 1 | . | C | 35.0% | 135.3 / 143.4 | 80 | coding (527/822 nt) | nimR | DNA‑binding transcriptional repressor NimR |
| * | NC_000913 | 3,423,287 | 0 | G | C | 35.0% | 67.2 / 15.3 | 41 | intergenic (+93/+136) | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA |
| * | NC_000913 | 3,355,999 | 0 | G | A | 33.8% | 170.6 / 144.9 | 136 | W425* (TGG→TGA) | gltB | glutamate synthase subunit GltB |
| * | NC_000913 | 589,934 | 0 | T | G | 32.9% | 169.4 / 21.0 | 86 | T341P (ACC→CCC) | nfrA | bacteriophage N4 receptor, outer membrane protein |
| * | NC_000913 | 2,915,727 | 0 | G | A | 32.8% | 158.3 / 128.9 | 122 | R224Q (CGG→CAG) | barA | sensory histidine kinase BarA |
| * | NC_000913 | 4,070,462 | 0 | T | C | 31.9% | 160.8 / 118.6 | 121 | intergenic (‑61/+53) | yihR/yihS | putative aldose 1‑epimerase YihR/sulfoquinovose isomerase |
| * | NC_000913 | 1,955,693 | 0 | G | A | 31.7% | 157.0 / 99.3 | 104 | P439S (CCT→TCT) | torZ | trimethylamine N‑oxide reductase 2 |
| * | NC_000913 | 1,944,197 | 0 | T | C | 30.8% | 250.6 / 146.4 | 156 | *262Q (TAA→CAA) | znuB | Zn(2(+)) ABC transporter membrane subunit |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.0% | 472.6 / 287.9 | 297 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 599,576 | 0 | T | G | 28.7% | 198.7 / 18.0 | 88 | V288G (GTG→GGG) | cusA | copper/silver export system RND permease |
| * | NC_000913 | 3,350,853 | 0 | A | C | 28.7% | 296.6 / 27.3 | 136 | S725A (TCA→GCA) | arcB | sensory histidine kinase ArcB |
| * | NC_000913 | 987,494 | 0 | T | G | 27.6% | 174.6 / 17.1 | 77 | intergenic (‑512/+91) | ompF/asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3593298 | 107 (0.980) | 25 (0.230) | 23/98 | 4.7 | 19.2% | coding (140/714 nt) | livF | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF |
| ? | NC_000913 | 3593309 = | 104 (0.950) | coding (129/714 nt) | livF | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF | |||||
| * | ? | NC_000913 | = 4400288 | 150 (1.370) | 25 (0.240) | 20/94 | 5.2 | 14.8% | coding (1/309 nt) | hfq | RNA‑binding protein Hfq |
| ? | NC_000913 | 4400296 = | 144 (1.370) | coding (9/309 nt) | hfq | RNA‑binding protein Hfq | |||||
| * | ? | NC_000913 | 3155097 = | 170 (1.550) | 69 (0.660) | 18/94 | 5.9 | 32.4% | coding (122/957 nt) | yqhC | DNA‑binding transcriptional activator YqhC |
| ? | NC_000913 | = 4171979 | 125 (1.190) | intergenic (+223/‑78) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 1207790 = | 4 (0.040) | 8 (0.110) | 7/66 | 7.8 | 81.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 1 (0.010) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 3593298 | 107 (0.980) | 9 (0.110) +CCCCGCCCCGT |
7/76 | 9.1 | 9.3% | coding (140/714 nt) | livF | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF |
| ? | NC_000913 | = 3638023 | 122 (1.110) | coding (382/1500 nt) | pitA | metal phosphate:H(+) symporter PitA | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 8 (0.090) | 7/82 | 9.8 | 100% | intergenic (‑305/+16) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 1994264 = | 128 (1.170) | 240 (3.090) +ATTTCTAATGTCGT |
3/70 | 11.4 | 72.6% | coding (443/1833 nt) | uvrC | excision nuclease subunit C |
| ? | NC_000913 | 3208976 = | 128 (1.170) | coding (953/1464 nt) | ttdT | L‑tartrate:succinate antiporter | |||||
| * | ? | NC_000913 | 4168431 = | 0 (0.000) | 3 (0.040) | 3/74 | 11.9 | 100% | noncoding (60/76 nt) | gltT | tRNA‑Glu |
| ? | NC_000913 | 4209845 = | NA (NA) | noncoding (72/76 nt) | gltV | tRNA‑Glu | |||||
| * | ? | NC_000913 | 3943494 = | NA (NA) | 3 (0.040) | 3/74 | 11.9 | NA | noncoding (60/76 nt) | gltU | tRNA‑Glu |
| ? | NC_000913 | 3943506 = | NA (NA) | noncoding (72/76 nt) | gltU | tRNA‑Glu | |||||
| * | ? | NC_000913 | = 2729385 | 0 (0.000) | 3 (0.040) | 3/74 | 11.9 | 100% | noncoding (60/76 nt) | gltW | tRNA‑Glu |
| ? | NC_000913 | 3943506 = | NA (NA) | noncoding (72/76 nt) | gltU | tRNA‑Glu | |||||