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 39 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 58,065 | 0 | C | A | 37.9% | 135.9 / 24.0 | 103 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,097,118 | 0 | C | A | 37.5% | 28.0 / 37.9 | 48 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,911,533 | 0 | C | A | 37.2% | 244.5 / 20.5 | 148 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,289,087 | 0 | A | . | 36.0% | 282.6 / 219.3 | 136 | coding (274/2517 nt) | yraJ | putative fimbrial usher protein YraJ |
| * | NC_000913 | 4,360,965 | 0 | C | A | 35.7% | 206.6 / 25.1 | 129 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,477,265 | 0 | A | C | 35.3% | 86.8 / 21.9 | 68 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 4,296,268 | 0 | T | C | 34.4% | 22.4 / 21.0 | 32 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,427,822 | 0 | C | A | 33.8% | 227.8 / 16.5 | 133 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 2,722,838 | 0 | G | T | 33.3% | 190.1 / 12.6 | 117 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 1,631,903 | 0 | G | T | 32.3% | 135.3 / 14.6 | 96 | S128Y (TCC→TAC) | ydfJ | putative transporter YdfJ |
| * | NC_000913 | 2,288,418 | 0 | G | T | 32.0% | 231.3 / 25.6 | 150 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 3,054,894 | 0 | G | T | 31.9% | 127.1 / 24.9 | 91 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,153,502 | 0 | C | A | 31.7% | 193.7 / 10.5 | 104 | intergenic (+79/‑61) | metC/yghB | cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase/DedA family protein YghB |
| * | NC_000913 | 2,990,480 | 0 | C | A | 31.6% | 178.0 / 18.2 | 117 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 1,779,583 | 0 | G | T | 31.5% | 174.9 / 15.1 | 108 | intergenic (‑282/‑34) | ydiP/ydiQ | putative DNA‑binding transcriptional regulator YdiP/putative electron transfer flavoprotein subunit YdiQ |
| * | NC_000913 | 847,955 | 0 | G | A | 30.8% | 205.0 / 54.7 | 147 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 240,066 | 0 | C | A | 30.4% | 196.8 / 11.6 | 112 | E42* (GAG→TAG) | yafV | 2‑oxoglutaramate amidase |
| * | NC_000913 | 58,594 | 0 | G | T | 29.9% | 262.3 / 13.4 | 144 | E41* (GAG→TAG) | yabP | putative uncharacterized protein YabP |
| * | NC_000913 | 2,895,349 | 0 | G | T | 29.3% | 130.0 / 15.6 | 75 | P144Q (CCG→CAG) | ygcQ | putative flavoprotein |
| * | NC_000913 | 1,756,353 | 0 | C | A | 29.0% | 219.9 / 15.1 | 131 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| Marginal new junction evidence (lowest skew 10 of 52 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1293196 = | 92 (0.990) | 21 (0.230) | 17/590 | 3.7 | 18.6% | intergenic (‑274/‑331) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 25 (0.270) | 16/590 | 3.9 | 19.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4497970 = | 103 (1.110) | intergenic (+1481/‑302) | leuX/insC6 | tRNA‑Leu/IS2 insertion element repressor InsA | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 22 (0.240) | 15/590 | 4.1 | 17.6% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 572729 = | 103 (1.110) | coding (264/456 nt) | ybcN | DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 781369 = | 74 (0.800) | 9 (0.130) | 9/434 | 4.3 | 14.5% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521252 | 52 (0.760) | intergenic (+4/‑1) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 3648146 | 122 (1.320) | 12 (0.160) | 10/474 | 4.4 | 10.8% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 101 (1.360) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2653419 | 77 (0.830) | 14 (0.170) | 12/540 | 4.4 | 15.9% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 78 (0.920) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 3960103 | 171 (1.840) | 21 (0.230) | 13/590 | 4.6 | 10.9% | intergenic (‑290/‑574) | ppiC/rep | peptidyl‑prolyl cis‑trans isomerase C/ATP‑dependent DNA helicase Rep |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 16 (0.170) | 13/588 | 4.6 | 9.2% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3722142 | 158 (1.710) | intergenic (+93/+186) | insK/glyS | IS150 family conserved protein InsB/glycine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_000913 | = 2558698 | 64 (0.690) | 14 (0.160) | 12/574 | 4.7 | 18.5% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 61 (0.680) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | = 696741 | 65 (0.700) | 9 (0.130) | 7/434 | 5.0 | 15.3% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 52 (0.760) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||