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 45 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,166,860 | 0 | G | A | 52.7% | 8.0 / 72.8 | 57 | noncoding (202/1542 nt) | rrsB | 16S ribosomal RNA |
| * | NC_000913 | 3,054,888 | 0 | A | C | 38.5% | 189.2 / 16.2 | 124 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,611,507 | 0 | G | T | 36.4% | 234.4 / 20.1 | 140 | L116L (CTC→CTA) | dgcF | putative diguanylate cyclase DgcF |
| * | NC_000913 | 1,922,815 | 0 | C | A | 36.4% | 154.2 / 31.3 | 129 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 3,054,894 | 0 | G | T | 35.7% | 152.8 / 53.9 | 126 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.6% | 262.1 / 23.4 | 162 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.1% | 147.1 / 26.1 | 91 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,767,444 | 0 | C | A | 33.1% | 275.9 / 18.6 | 131 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,443 | 0 | C | A | 32.6% | 283.9 / 10.9 | 131 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,054,886 | 0 | G | T | 32.5% | 197.8 / 43.1 | 124 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,097,118 | 0 | C | A | 30.9% | 35.4 / 23.4 | 42 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,767,445 | 0 | C | A | 30.5% | 278.3 / 18.6 | 131 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 4,360,965 | 0 | C | A | 30.1% | 299.2 / 20.0 | 146 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 3,420,669 | 0 | G | T | 29.4% | 259.5 / 12.9 | 136 | G179V (GGA→GTA) | yhdX | putative ABC transporter membrane subunit YhdX |
| * | NC_000913 | 3,970,253 | 0 | G | T | 28.9% | 329.9 / 14.9 | 159 | E41* (GAG→TAG) | wecB | UDP‑N‑acetylglucosamine 2‑epimerase |
| * | NC_000913 | 2,457,177 | 0 | T | G | 28.8% | 127.5 / 11.9 | 76 | G661G (GGA→GGC) | fadJ | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| * | NC_000913 | 2,472,817 | 0 | C | A | 28.4% | 189.3 / 10.8 | 88 | G22V (GGA→GTA) | yfdN | uncharacterized protein YfdN |
| * | NC_000913 | 147,802 | 0 | C | A | 28.1% | 260.3 / 10.2 | 135 | R279R (CGG→AGG) | rpnC | recombination‑promoting nuclease RpnC |
| * | NC_000913 | 1,334,966 | 0 | A | C | 27.2% | 341.8 / 37.6 | 195 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 2,073,613 | 0 | G | T | 27.2% | 200.4 / 19.7 | 103 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 102 (0.820) | 11 (0.130) | 9/420 | 6.0 | 13.5% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 69 (0.790) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 780629 | 102 (0.820) | 12 (0.130) | 10/446 | 6.0 | 15.5% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 55 (0.600) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 781222 | 43 (0.350) | 6 (0.060) | 6/446 | 7.7 | 9.9% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 77 (0.830) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2357652 | 134 (1.080) | 7 (0.060) | 7/530 | 8.3 | 5.7% | coding (749/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357836 = | 112 (1.020) | intergenic (+33/+206) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1286906 | 66 (0.530) | 8 (0.070) | 6/558 | 9.1 | 9.9% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 84 (0.730) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2817942 | 83 (0.670) | 5 (0.040) | 4/558 | 10.2 | 6.2% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 75 (0.650) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 4542690 | 212 (1.710) | 5 (0.040) | 4/580 | 10.5 | 2.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 176 (1.470) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4295870 | 83 (0.670) | 3 (0.030) | 3/520 | 10.5 | 3.5% | intergenic (+76/+566) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | 4296434 = | 91 (0.840) | intergenic (+640/+2) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||
| * | ? | NC_000913 | = 2904285 | 128 (1.030) | 3 (0.030) | 3/542 | 10.7 | 2.6% | intergenic (+911/+462) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| ? | NC_000913 | 2904347 = | 109 (0.970) | intergenic (+973/+400) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE | |||||
| * | ? | NC_000913 | = 2976192 | 179 (1.450) | 3 (0.030) | 3/562 | 10.9 | 2.0% | intergenic (‑3/+112) | omrA/omrB | small regulatory RNA OmrA/small regulatory RNA OmrB |
| ? | NC_000913 | 2976389 = | 130 (1.120) | intergenic (‑4/‑210) | omrB/galR | small regulatory RNA OmrB/DNA‑binding transcriptional dual regulator GalR | |||||