mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 67 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 190,843 | 0 | C | A | 42.3% | 146.8 / 16.8 | 130 | intergenic (+244/‑14) | rpsB/tsf | 30S ribosomal subunit protein S2/protein chain elongation factor EF‑Ts |
| * | NC_000913 | 2,493,432 | 0 | G | C | 42.1% | 16.8 / 50.7 | 38 | intergenic (‑178/+335) | frc/yfdX | formyl‑CoA transferase/protein YfdX |
| * | NC_000913 | 2,477,265 | 0 | A | C | 39.4% | 182.2 / 48.5 | 127 | L122* (TTA→TGA) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,472,817 | 0 | C | A | 36.5% | 153.0 / 11.8 | 96 | G22V (GGA→GTA) | yfdN | uncharacterized protein YfdN |
| * | NC_000913 | 1,427,992 | 0 | G | T | 35.2% | 213.4 / 21.6 | 159 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 1,375,723 | 0 | C | A | 34.9% | 167.5 / 14.4 | 106 | S254Y (TCC→TAC) | ycjQ | D‑guloside 3‑dehydrogenase |
| * | NC_000913 | 58,065 | 0 | C | A | 34.6% | 223.8 / 24.9 | 129 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 320,845 | 0 | C | A | 34.0% | 126.4 / 16.4 | 97 | R207R (CGG→AGG) | rclR | DNA‑binding transcriptional activator RclR |
| * | NC_000913 | 442,471 | 0 | C | A | 33.8% | 210.1 / 13.8 | 139 | S308Y (TCC→TAC) | thiI | tRNA uridine 4‑sulfurtransferase |
| * | NC_000913 | 2,288,418 | 0 | G | T | 33.7% | 277.8 / 28.3 | 166 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 3,741,871 | 0 | G | T | 33.1% | 263.8 / 29.7 | 157 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 1,922,815 | 0 | C | A | 31.6% | 241.5 / 19.2 | 139 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,767,445 | 0 | C | A | 31.4% | 240.7 / 27.3 | 121 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,990,480 | 0 | C | A | 30.5% | 324.4 / 11.3 | 190 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 1,351,463 | 0 | C | A | 30.2% | 217.2 / 18.7 | 139 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 2,477,264 | 0 | T | C | 30.2% | 253.4 / 10.7 | 127 | L122L (TTA→TTG) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,722,838 | 0 | G | T | 29.7% | 276.3 / 12.3 | 145 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 3,115,105 | 0 | G | T | 29.6% | 206.8 / 12.6 | 108 | L1336L (CTC→CTA) | yghJ | putative lipoprotein YghJ |
| * | NC_000913 | 1,756,353 | 0 | C | A | 29.3% | 259.6 / 14.1 | 150 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| * | NC_000913 | 3,911,533 | 0 | C | A | 29.1% | 301.8 / 21.5 | 175 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 780629 | 125 (1.010) | 27 (0.290) | 21/436 | 3.1 | 23.1% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 87 (0.950) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 1287329 | 73 (0.590) | 11 (0.130) | 11/414 | 5.3 | 17.3% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 54 (0.620) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 3648146 | 140 (1.130) | 14 (0.140) | 12/472 | 5.7 | 10.8% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 118 (1.190) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 4542690 | 189 (1.530) | 16 (0.130) | 14/570 | 6.2 | 9.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 142 (1.180) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4606166 | 97 (0.780) | 9 (0.100) | 8/410 | 6.4 | 11.1% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 77 (0.890) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | 4542682 = | 176 (1.420) | 13 (0.110) | 13/570 | 6.5 | 7.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 143 (1.190) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2653419 | 111 (0.900) | 13 (0.110) | 11/538 | 6.9 | 10.6% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 117 (1.030) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2947467 | 93 (0.750) | 8 (0.090) | 7/422 | 7.0 | 10.5% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 69 (0.780) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 2518116 | 95 (0.770) | 7 (0.080) | 7/426 | 7.0 | 9.9% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 58 (0.650) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 781016 | 88 (0.710) | 13 (0.120) | 9/514 | 7.3 | 13.2% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
| ? | NC_000913 | 781809 = | 94 (0.870) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||