mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 29 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP006584 | 1,563,237 | 0 | T | C | 73.9% | 32.9 / 26.9 | 46 | V173A (GTT→GCT) | LY180_07445 | transposase IS609 |
| * | CP006584 | 1,643,582 | 0 | G | A | 65.2% | 154.4 / 144.9 | 155 | intergenic (‑242/‑61) | LY180_07760/LY180_07765 | sulfatase/transposase |
| * | CP006584 | 1,563,136 | 0 | T | C | 60.9% | ‑5.7 / 20.3 | 24 | N139N (AAT→AAC) | LY180_07445 | transposase IS609 |
| * | CP006584 | 269,400 | 0 | G | A | 53.3% | 1.7 / 152.7 | 120 | E42E (GAG→GAA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,438 | 0 | T | C | 52.6% | ‑4.4 / 175.5 | 136 | L55P (CTC→CCC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,403 | 0 | T | C | 52.1% | ‑3.2 / 150.1 | 121 | G43G (GGT→GGC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,452 | 0 | C | T | 50.7% | 18.8 / 199.2 | 138 | Q60* (CAA→TAA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,443 | 0 | T | G | 49.6% | ‑3.0 / 228.6 | 137 | F57V (TTT→GTT) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,492 | 0 | C | T | 49.2% | 30.7 / 183.9 | 132 | T73I (ACC→ATC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,453 | 0 | A | G | 48.2% | 19.2 / 200.2 | 140 | Q60R (CAA→CGA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,116 | 0 | C | T | 41.0% | 55.5 / 128.6 | 119 | R121R (CGC→CGT) | LY180_01180 | hypothetical protein |
| * | CP006584 | 1,310,832 | 0 | T | G | 41.0% | 69.3 / 94.1 | 78 | intergenic (‑288/+141) | LY180_06180/LY180_06185 | hypothetical protein/hypothetical protein |
| * | CP006584 | 1,310,833 | 0 | A | G | 40.8% | 57.6 / 84.3 | 78 | intergenic (‑289/+140) | LY180_06180/LY180_06185 | hypothetical protein/hypothetical protein |
| * | CP006584 | 4,253,902 | 0 | C | T | 37.5% | 135.2 / 136.8 | 142 | intergenic (+24/‑40) | LY180_20335/LY180_20340 | hypothetical protein/hypothetical protein |
| * | CP006584 | 4,253,976 | 0 | T | A | 37.3% | 136.9 / 151.8 | 136 | F12Y (TTC→TAC) | LY180_20340 | hypothetical protein |
| * | CP006584 | 269,044 | 0 | T | C | 35.3% | 69.6 / 96.0 | 102 | C97C (TGT→TGC) | LY180_01180 | hypothetical protein |
| * | CP006584 | 269,041 | 0 | T | C | 35.0% | 81.1 / 91.5 | 102 | D96D (GAT→GAC) | LY180_01180 | hypothetical protein |
| * | CP006584 | 4,253,879 | 0 | G | A | 34.1% | 159.3 / 118.9 | 132 | intergenic (+1/‑63) | LY180_20335/LY180_20340 | hypothetical protein/hypothetical protein |
| * | CP006584 | 1,643,618 | 0 | C | G | 32.6% | 176.3 / 136.7 | 140 | intergenic (‑278/‑25) | LY180_07760/LY180_07765 | sulfatase/transposase |
| * | CP006584 | 4,254,025 | 0 | G | A | 32.0% | 151.3 / 103.5 | 129 | A28A (GCG→GCA) | LY180_20340 | hypothetical protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP006584 | = 3513964 | 24 (0.380) | 0 (0.000) +275 bp |
3/38 | 0.2 | 0.0% | intergenic (‑140/+199) | tldD/LY180_16725 | protease TldD/membrane protein |
| ? | CP006584 | 3513966 = | 24 (0.380) | intergenic (‑142/+197) | tldD/LY180_16725 | protease TldD/membrane protein | |||||
| * | ? | CP006584 | = 4739815 | 74 (1.170) | 9 (0.150) | 9/570 | 4.5 | 11.3% | intergenic (+56/‑424) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A |
| ? | CP006584 | = 4740111 | 69 (1.130) | intergenic (+352/‑128) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A | |||||
| * | ? | CP006584 | 4739807 = | 74 (1.170) | 8 (0.130) | 8/570 | 4.8 | 10.2% | intergenic (+48/‑432) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A |
| ? | CP006584 | 4740121 = | 69 (1.130) | intergenic (+362/‑118) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A | |||||
| * | ? | CP006584 | 2921410 = | 65 (1.030) | 3 (0.050) | 3/582 | 6.9 | 4.4% | coding (1099/1365 nt) | LY180_13900 | transporter |
| ? | CP006584 | = 4359965 | 65 (1.040) | intergenic (+51/‑64) | LY180_20870/tuf | tRNA‑Thr/elongation factor Tu | |||||
| * | ? | CP006584 | 2390946 = | 54 (0.850) | 3 (0.050) | 3/586 | 6.9 | 4.7% | coding (1262/1761 nt) | LY180_11415 | hypothetical protein |
| ? | CP006584 | 4374441 = | 69 (1.100) | coding (592/1134 nt) | thiH | thiamine biosynthesis protein ThiH | |||||
| * | ? | CP006584 | = 115117 | 95 (1.500) | 3 (0.050) | 3/584 | 6.9 | 3.4% | coding (115/1044 nt) | LY180_00505 | guanosine 5'‑monophosphate oxidoreductase |
| ? | CP006584 | = 4090000 | 76 (1.210) | coding (1163/1521 nt) | LY180_19505 | ATP‑dependent protease | |||||
| * | ? | CP006584 | = 7939 | 73 (1.160) | 3 (0.050) | 3/584 | 6.9 | 4.8% | coding (1299/1431 nt) | LY180_00040 | sodium:alanine symporter |
| ? | CP006584 | 2844541 = | 47 (0.750) | coding (135/1401 nt) | LY180_13490 | gamma‑aminobutyrate transporter | |||||
| * | ? | CP006584 | 4496330 = | NA (NA) | 3 (0.050) | 3/588 | 7.0 | 4.6% | coding (120/1209 nt) | LY180_21450 | hypothetical protein |
| ? | CP006584 | 4508827 = | 62 (0.980) | coding (95/681 nt) | LY180_21520 | phosphonate ABC transporter ATP‑binding protein | |||||