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 35 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,427,992 | 0 | G | T | 43.0% | 121.4 / 14.1 | 93 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 3,911,533 | 0 | C | A | 39.4% | 107.8 / 20.8 | 94 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 12,152 | 0 | G | T | 36.3% | 109.6 / 13.4 | 91 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 58,065 | 0 | C | A | 34.4% | 151.2 / 14.2 | 93 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,922,815 | 0 | C | A | 33.0% | 182.3 / 21.8 | 112 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,722,838 | 0 | G | T | 31.8% | 192.3 / 10.6 | 107 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 2,304,798 | 0 | T | C | 31.2% | 38.0 / 17.4 | 32 | intergenic (+405/+310) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 3,741,871 | 0 | G | T | 30.4% | 164.2 / 10.9 | 92 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,477,265 | 0 | A | C | 30.0% | 128.1 / 17.8 | 71 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 4,100,801 | 0 | G | T | 29.0% | 138.1 / 13.3 | 93 | intergenic (‑276/‑9) | rhaT/sodA | rhamnose/lyxose:H(+) symporter/superoxide dismutase (Mn) |
| * | NC_000913 | 2,990,480 | 0 | C | A | 28.8% | 225.4 / 11.5 | 126 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 4,136,467 | 0 | A | C | 28.8% | 113.1 / 21.8 | 75 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 3,896,780 | 0 | C | A | 28.6% | 184.0 / 12.1 | 98 | R3R (CGG→AGG) | yieH | 6‑phosphogluconate phosphatase |
| * | NC_000913 | 3,032,307 | 0 | C | T | 28.4% | 150.9 / 26.9 | 88 | T314M (ACG→ATG) | uacT | urate:H(+) symporter |
| * | NC_000913 | 1,657,157 | 0 | C | A | 28.4% | 223.6 / 21.7 | 134 | E101* (GAG→TAG) | ynfC | PF06788 family lipoprotein YnfC |
| * | NC_000913 | 2,767,445 | 0 | C | A | 27.8% | 231.7 / 10.9 | 98 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,054,894 | 0 | G | T | 27.8% | 107.9 / 11.7 | 72 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,015,488 | 0 | C | A | 27.5% | 205.7 / 13.0 | 131 | intergenic (+29/‑227) | pqiC/rmf | intermembrane transport lipoprotein PqiC/ribosome modulation factor |
| * | NC_000913 | 4,360,965 | 0 | C | A | 27.1% | 229.1 / 10.9 | 108 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 1,502,770 | 0 | T | C | 26.7% | 158.1 / 24.5 | 102 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3648146 | 91 (1.060) | 11 (0.160) | 11/472 | 4.0 | 12.6% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 79 (1.140) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2518116 | 70 (0.810) | 7 (0.110) | 6/426 | 5.2 | 12.4% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 48 (0.770) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 781222 | 64 (0.740) | 6 (0.090) | 6/436 | 5.4 | 11.3% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 47 (0.740) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 3708466 | 49 (0.570) | 4 (0.070) | 4/372 | 5.6 | 10.7% | intergenic (‑761/+150) | dppA/proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| ? | NC_000913 | 3708635 = | 36 (0.660) | noncoding (58/77 nt) | proK | tRNA‑Pro | |||||
| * | ? | NC_000913 | = 696469 | 67 (0.780) | 13 (0.150) +TAGAAT |
9/576 | 5.6 | 17.9% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696802 = | 55 (0.640) | noncoding (29/75 nt) | glnW | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 2521006 | 73 (0.850) | 7 (0.110) | 5/436 | 5.8 | 12.2% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521249 = | 47 (0.740) | intergenic (+1/‑4) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 2357730 | 93 (1.080) | 8 (0.110) | 6/508 | 6.1 | 8.6% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 89 (1.200) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1286906 | 53 (0.620) | 8 (0.100) | 7/548 | 6.1 | 14.8% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 43 (0.540) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2653502 | 80 (0.930) | 7 (0.090) | 6/520 | 6.2 | 9.5% | intergenic (‑47/‑353) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| ? | NC_000913 | 2653825 = | 62 (0.810) | intergenic (‑370/‑30) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 781446 | 71 (0.830) | 4 (0.060) | 4/432 | 6.3 | 7.5% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 46 (0.730) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||