mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 847,955 | 0 | G | A | 38.0% | 144.7 / 79.2 | 143 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 58,065 | 0 | C | A | 35.7% | 120.6 / 16.1 | 84 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,741,871 | 0 | G | T | 33.9% | 184.1 / 17.0 | 118 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 1,611,507 | 0 | G | T | 32.6% | 117.2 / 10.9 | 86 | L116L (CTC→CTA) | dgcF | putative diguanylate cyclase DgcF |
| * | NC_000913 | 3,911,533 | 0 | C | A | 32.4% | 220.1 / 13.8 | 136 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,465,016 | 0 | C | A | 32.1% | 178.2 / 13.7 | 106 | intergenic (‑9/‑285) | mlaA/yfdC | intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA/inner membrane protein YfdC |
| * | NC_000913 | 1,466,438 | 0 | T | G | 31.8% | 98.4 / 41.4 | 63 | pseudogene (1047/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 2,767,445 | 0 | C | A | 30.9% | 181.8 / 14.3 | 81 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,477,265 | 0 | A | C | 30.0% | 164.1 / 16.1 | 90 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,351,463 | 0 | C | A | 29.7% | 137.7 / 11.0 | 91 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 4,074,572 | 0 | C | A | 29.5% | 195.7 / 11.5 | 112 | P278P (CCC→CCA) | yihV | 6‑deoxy‑6‑sulfofructose kinase |
| * | NC_000913 | 2,326,713 | 0 | C | A | 29.4% | 183.1 / 12.6 | 102 | P202Q (CCG→CAG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,466,432 | 0 | A | G | 28.6% | 119.3 / 36.5 | 63 | pseudogene (1041/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 2,990,480 | 0 | C | A | 28.4% | 263.9 / 15.6 | 148 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 4,261,040 | 0 | C | A | 27.6% | 257.9 / 11.1 | 127 | Q148K (CAA→AAA) | yjbM | DUF2713 domain‑containing protein YjbM |
| * | NC_000913 | 3,768,435 | 0 | C | A | 27.5% | 328.9 / 13.5 | 160 | Q87K (CAG→AAG) | yibG | tetratricopeptide‑like domain‑containing protein YibG |
| * | NC_000913 | 2,270,138 | 0 | C | A | 27.4% | 219.8 / 11.7 | 113 | Q54K (CAG→AAG) | mepS | peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| * | NC_000913 | 1,097,118 | 0 | C | A | 27.1% | 69.2 / 40.5 | 59 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,466,418 | 0 | A | G | 27.0% | 135.3 / 33.4 | 63 | pseudogene (1027/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 2,178,156 | 0 | C | A | 26.7% | 200.9 / 14.4 | 101 | E137* (GAG→TAG) | fbaB | fructose‑bisphosphate aldolase class I |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1287084 | 64 (0.710) | 13 (0.160) | 9/546 | 5.3 | 17.8% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 60 (0.720) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1286906 | 57 (0.630) | 10 (0.120) | 9/546 | 5.3 | 15.0% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 60 (0.720) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 3764827 | NA (NA) | 10 (0.120) | 9/562 | 5.4 | 72.3% | coding (2645/4134 nt) | rhsA | rhs element protein RhsA |
| ? | NC_000913 | 3765008 = | 4 (0.040) | coding (2826/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 732239 | 71 (0.790) | 10 (0.120) | 9/562 | 5.4 | 21.7% | coding (2657/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | 3765020 = | 4 (0.050) | coding (2838/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 2947467 | 47 (0.520) | 6 (0.090) | 5/420 | 5.6 | 14.7% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 36 (0.560) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 696741 | 61 (0.680) | 5 (0.080) | 5/430 | 5.7 | 8.7% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 60 (0.910) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 3621836 | NA (NA) | 9 (0.100) | 8/562 | 5.8 | 82.4% | coding (2645/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3622017 = | 2 (0.020) | coding (2826/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 732239 | 71 (0.790) | 9 (0.100) | 8/562 | 5.8 | 20.4% | coding (2657/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | 3622029 = | 2 (0.020) | coding (2838/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 4542682 = | 159 (1.770) | 9 (0.100) | 7/568 | 6.2 | 6.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 122 (1.400) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2518116 | 72 (0.800) | 5 (0.080) | 4/424 | 6.2 | 8.8% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 52 (0.800) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||