mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 31 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AP012306 | 1,091,992 | 0 | T | G | 36.7% | 373.7 / 54.6 | 196 | intergenic (+38/‑145) | narI/ychS | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/predicted protein |
| * | AP012306 | 1,944,288 | 0 | A | C | 36.1% | 377.5 / 50.7 | 206 | G361G (GGT→GGG) | menE | o‑succinylbenzoate‑CoA ligase |
| * | AP012306 | 3,527,368 | 0 | A | C | 33.3% | 555.5 / 71.5 | 261 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator, L‑rhamnose‑binding |
| * | AP012306 | 644,417 | 0 | G | A | 31.9% | 743.0 / inf | 514 | intergenic (+32/‑401) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| * | AP012306 | 202,417 | 0 | T | G | 31.5% | 428.2 / 32.7 | 213 | V409G (GTA→GGA) | tilS | tRNA(Ile)‑lysidine synthetase |
| * | AP012306 | 1,854,851 | 0 | A | C | 31.0% | 559.9 / 94.0 | 258 | T25P (ACC→CCC) | yejH | predicted ATP‑dependet helicase |
| * | AP012306 | 2,758,909 | 0 | T | G | 30.6% | 449.4 / 14.3 | 193 | G33G (GGT→GGG) | agaD | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
| * | AP012306 | 935,054 | 0 | G | T | 30.6% | 168.0 / 38.1 | 72 | intergenic (+24/‑1406) | putP/ycdO | proline:sodium symporter/conserved protein |
| * | AP012306 | 1,128,412 | 0 | T | G | 30.0% | 591.7 / 64.0 | 270 | V29G (GTG→GGG) | yciO | conserved protein |
| * | AP012306 | 2,212,753 | 0 | A | C | 29.8% | 262.9 / 51.4 | 121 | Y241D (TAT→GAT) | hcaT | predicted 3‑phenylpropionic transporter |
| * | AP012306 | 3,938,887 | 0 | C | T | 28.4% | 532.7 / 170.5 | 271 | S44F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator |
| * | AP012306 | 341,377 | 0 | T | G | 27.8% | 219.1 / 19.3 | 108 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | AP012306 | 800,675 | 0 | A | C | 26.2% | 637.0 / 47.2 | 264 | T192P (ACC→CCC) | lolA | chaperone for lipoproteins |
| * | AP012306 | 3,903,791 | 0 | A | G | 25.7% | 568.4 / 70.4 | 245 | E189G (GAA→GGA) | yjgJ | predicted transcriptional regulator |
| * | AP012306 | 257,137 | 0 | T | G | 25.6% | 379.3 / 10.8 | 176 | L496V (TTG→GTG) | betT | choline transporter of high affinity |
| * | AP012306 | 3,182,861 | 0 | A | C | 25.4% | 284.6 / 23.5 | 114 | L198F (TTA→TTC) | yiaN | predicted transporter |
| * | AP012306 | 3,590,367 | 0 | A | C | 25.4% | 734.4 / 44.1 | 276 | T30P (ACC→CCC) | fabR | DNA‑binding transcriptional repressor |
| * | AP012306 | 1,226,557 | 0 | A | G | 24.9% | 397.1 / 75.5 | 177 | G55G (GGA→GGG) | ydcU | predicted spermidine/putrescine transporter subunit |
| * | AP012306 | 2,714,555 | 0 | T | G | 24.3% | 745.6 / 17.8 | 304 | T175P (ACC→CCC) | ygjV | conserved inner membrane protein |
| * | AP012306 | 472,868 | 0 | T | G | 24.2% | 562.8 / 19.7 | 211 | D435A (GAC→GCC) | cusS | sensory histidine kinase in two‑component regulatory system with CusR, senses copper ions |
| Marginal new junction evidence (lowest skew 10 of 78 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AP012306 | = 1092512 | 320 (1.040) | 22 (0.080) | 14/258 | 7.7 | 7.2% | intergenic (+100/+3) | ychS/tpr | predicted protein/predicted protamine‑like protein |
| ? | AP012306 | 1092985 = | 289 (1.090) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | AP012306 | = 997497 | 329 (1.070) | 10 (0.040) | 9/268 | 9.1 | 3.2% | coding (41/1305 nt) | ndh | respiratory NADH dehydrogenase 2/cupric reductase |
| ? | AP012306 | 997993 = | 313 (1.140) | coding (537/1305 nt) | ndh | respiratory NADH dehydrogenase 2/cupric reductase | |||||
| * | ? | AP012306 | = 215364 | NA (NA) | 8 (0.030) | 7/288 | 9.9 | NA | noncoding (745/2905 nt) | rrlH | 23S ribosomal RNA (rrlH) |
| ? | AP012306 | = 215372 | NA (NA) | noncoding (753/2905 nt) | rrlH | 23S ribosomal RNA (rrlH) | |||||
| * | ? | AP012306 | = 1382461 | 326 (1.060) | 6 (0.020) | 6/274 | 10.1 | 2.0% | coding (1524/1593 nt) | malX | fused maltose and glucose‑specific PTS enzyme IIBC components |
| ? | AP012306 | = 1382449 | 295 (1.050) | coding (1512/1593 nt) | malX | fused maltose and glucose‑specific PTS enzyme IIBC components | |||||
| * | ? | AP012306 | 3647856 = | 279 (0.910) | 6 (0.020) | 6/286 | 10.2 | 2.1% | coding (48/1737 nt) | aceK | isocitrate dehydrogenase kinase/phosphatase |
| ? | AP012306 | 3647888 = | 281 (0.960) | coding (80/1737 nt) | aceK | isocitrate dehydrogenase kinase/phosphatase | |||||
| * | ? | AP012306 | 2261845 = | 374 (1.220) | 5 (0.020) | 5/270 | 10.4 | 1.4% | coding (232/384 nt) | yfiD | pyruvate formate lyase subunit |
| ? | AP012306 | 2261859 = | 345 (1.240) | coding (218/384 nt) | yfiD | pyruvate formate lyase subunit | |||||
| * | ? | AP012306 | 3597334 = | 140 (0.460) | 5 (0.020) | 5/290 | 10.6 | 2.8% | noncoding (1463/1542 nt) | rrsB | 16S ribosomal RNA (rrnB) |
| ? | AP012306 | 3597372 = | 214 (0.720) | noncoding (1501/1542 nt) | rrsB | 16S ribosomal RNA (rrnB) | |||||
| * | ? | AP012306 | 3466240 = | 188 (0.610) | 5 (0.020) | 5/290 | 10.6 | 3.0% | noncoding (1497/1542 nt) | rrsA | 16S ribosomal RNA (rrnA) |
| ? | AP012306 | 3597338 = | 140 (0.470) | noncoding (1467/1542 nt) | rrsB | 16S ribosomal RNA (rrnB) | |||||
| * | ? | AP012306 | = 2895148 | NA (NA) | 5 (0.020) | 5/290 | 10.6 | 2.3% | noncoding (1467/1542 nt) | rrsD | 16S ribosomal RNA (rrnD) |
| ? | AP012306 | 3597368 = | 214 (0.700) | noncoding (1497/1542 nt) | rrsB | 16S ribosomal RNA (rrnB) | |||||
| * | ? | AP012306 | = 2895148 | NA (NA) | 5 (0.020) | 5/290 | 10.6 | 2.7% | noncoding (1467/1542 nt) | rrsD | 16S ribosomal RNA (rrnD) |
| ? | AP012306 | 3466240 = | 188 (0.610) | noncoding (1497/1542 nt) | rrsA | 16S ribosomal RNA (rrnA) | |||||