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 38 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,097,118 | 0 | C | A | 48.3% | ‑3.4 / 33.2 | 29 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 190,843 | 0 | C | A | 45.9% | 89.1 / 11.5 | 85 | intergenic (+244/‑14) | rpsB/tsf | 30S ribosomal subunit protein S2/protein chain elongation factor EF‑Ts |
| * | NC_000913 | 4,037,496 | 0 | A | T | 45.9% | 92.0 / 313.5 | 157 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 1,097,158 | 0 | C | T | 42.3% | 7.8 / 25.6 | 26 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,767,445 | 0 | C | A | 40.7% | 160.9 / 27.6 | 114 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,443 | 0 | C | A | 38.9% | 180.0 / 16.7 | 114 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,444 | 0 | C | A | 38.9% | 172.8 / 18.6 | 114 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 4,296,191 | 0 | A | C | 37.5% | 12.7 / 18.7 | 25 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,054,888 | 0 | A | C | 35.0% | 180.1 / 13.0 | 103 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.0% | 147.8 / 36.2 | 94 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,894 | 0 | G | T | 33.3% | 145.4 / 30.5 | 102 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,767,447 | 0 | C | A | 32.8% | 200.4 / 22.7 | 123 | intergenic (+92/‑263) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 58,065 | 0 | C | A | 32.7% | 163.8 / 22.1 | 104 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,922,815 | 0 | C | A | 32.1% | 133.4 / 22.8 | 84 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,767,449 | 0 | C | A | 31.1% | 211.8 / 20.7 | 123 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,902,613 | 0 | C | A | 30.7% | 141.8 / 12.8 | 75 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 847,955 | 0 | G | A | 30.4% | 162.2 / 56.1 | 125 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,741,871 | 0 | G | T | 30.2% | 218.0 / 14.0 | 119 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 4,427,822 | 0 | C | A | 30.1% | 288.4 / 21.2 | 156 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 3,054,886 | 0 | G | T | 29.1% | 177.4 / 24.5 | 103 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| Marginal new junction evidence (lowest skew 10 of 30 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 100 (1.070) | 15 (0.230) | 14/420 | 2.5 | 17.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 68 (1.040) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 156146 | 118 (1.260) | 15 (0.160) | 14/598 | 3.6 | 11.3% | coding (56/741 nt) | yadV | putative fimbrial chaperone YadV |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 17 (0.180) | 13/596 | 3.8 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3131469 = | 0 (0.000) | coding (940/1068 nt) | yghQ | putative transport protein YghQ | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 12 (0.130) | 11/596 | 4.2 | 13.8% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3489054 | 75 (0.800) | coding (1127/1221 nt) | argD | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase | |||||
| * | ? | NC_000913 | = 3366750 | NA (NA) | 10 (0.110) | 10/598 | 4.5 | 6.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3367046 = | 155 (1.660) | coding (121/717 nt) | yhcF | DUF1120 domain‑containing protein YhcF | |||||
| * | ? | NC_000913 | = 2357730 | 122 (1.300) | 8 (0.100) | 7/518 | 4.8 | 6.7% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 117 (1.440) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | 156143 = | 119 (1.270) | 9 (0.100) | 9/598 | 4.8 | 7.0% | coding (59/741 nt) | yadV | putative fimbrial chaperone YadV |
| ? | NC_000913 | = 275149 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3708466 | 86 (0.920) | 4 (0.070) | 4/382 | 4.9 | 7.0% | intergenic (‑761/+150) | dppA/proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| ? | NC_000913 | 3708635 = | 51 (0.850) | noncoding (58/77 nt) | proK | tRNA‑Pro | |||||
| * | ? | NC_000913 | = 4051345 | 85 (0.910) | 8 (0.090) | 8/594 | 5.0 | 8.6% | intergenic (+64/‑2) | csrC/yihI | small regulatory RNA CsrC/Der GTPase‑activating protein YihI |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2068408 = | 134 (1.440) | 9 (0.100) | 8/596 | 5.0 | 6.3% | intergenic (‑1123/‑227) | insH6/yoeA | IS5 family transposase and trans‑activator/TonB‑dependent receptor plug domain‑containing protein YoeA |
| ? | NC_000913 | 2068941 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||