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 50 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 | 47.4% | 96.4 / 13.9 | 95 | intergenic (+244/‑14) | rpsB/tsf | 30S ribosomal subunit protein S2/protein chain elongation factor EF‑Ts |
| * | NC_000913 | 3,054,894 | 0 | G | T | 35.2% | 129.7 / 33.2 | 105 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 33.0% | 190.9 / 43.9 | 112 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,886 | 0 | G | T | 32.7% | 172.8 / 34.0 | 105 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,911,533 | 0 | C | A | 32.6% | 207.5 / 27.5 | 135 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,602,706 | 0 | C | A | 31.1% | 69.0 / 47.1 | 74 | G14G (GGG→GGT) | ftsE | cell division protein FtsE |
| * | NC_000913 | 3,226,224 | 0 | G | T | 31.0% | 281.6 / 19.1 | 142 | intergenic (+53/‑10) | ebgC/ygjI | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI |
| * | NC_000913 | 4,074,572 | 0 | C | A | 30.8% | 170.6 / 17.2 | 107 | P278P (CCC→CCA) | yihV | 6‑deoxy‑6‑sulfofructose kinase |
| * | NC_000913 | 1,922,815 | 0 | C | A | 29.8% | 123.4 / 17.9 | 84 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 4,296,268 | 0 | T | C | 29.2% | 70.1 / 24.2 | 48 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,755,866 | 0 | G | A | 29.1% | 191.9 / 17.9 | 104 | noncoding (274/363 nt) | ssrA | tmRNA |
| * | NC_000913 | 1,902,806 | 0 | C | A | 28.9% | 230.5 / 11.4 | 136 | L253L (CTC→CTA) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 58,065 | 0 | C | A | 28.7% | 198.5 / 10.8 | 102 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,087,580 | 0 | G | A | 28.5% | 252.5 / 11.1 | 123 | N89N (AAC→AAT) | pgaC | poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC |
| * | NC_000913 | 161,559 | 0 | G | A | 28.4% | 169.2 / 10.9 | 81 | S158L (TCG→TTG) | thpR | RNA 2',3'‑cyclic phosphodiesterase |
| * | NC_000913 | 2,244,442 | 0 | C | A | 27.8% | 170.5 / 10.9 | 97 | P178Q (CCG→CAG) | yeiG | S‑formylglutathione hydrolase/S‑lactoylglutathione hydrolase |
| * | NC_000913 | 2,990,480 | 0 | C | A | 27.5% | 322.3 / 27.2 | 190 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 3,054,888 | 0 | A | C | 27.5% | 184.0 / 10.5 | 105 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,812,509 | 0 | G | T | 26.2% | 362.2 / 12.7 | 164 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 12,152 | 0 | G | T | 26.2% | 175.5 / 13.8 | 107 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| Marginal new junction evidence (lowest skew 10 of 56 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1287329 | 98 (0.890) | 6 (0.080) | 6/424 | 7.2 | 8.4% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 62 (0.790) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 696741 | 79 (0.720) | 8 (0.100) | 6/442 | 7.5 | 12.6% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 53 (0.650) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 3648146 | 136 (1.230) | 6 (0.070) | 6/482 | 8.0 | 5.2% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 108 (1.220) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 11 (0.100) | 9/598 | 8.0 | 8.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2454730 = | 117 (1.060) | intergenic (‑2394/+353) | yfcS/yfcV | putative fimbrial chaperone YfcS/putative fimbrial protein YfcV | |||||
| * | ? | NC_000913 | 4231665 = | 120 (1.090) | 9 (0.080) | 8/598 | 8.4 | 7.0% | intergenic (‑34/+219) | yjbD/lysC | DUF3811 domain‑containing protein YjbD/aspartate kinase III |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2691347 = | 134 (1.220) | 8 (0.070) | 8/592 | 8.4 | 5.7% | intergenic (‑7/+309) | glmY/purL | small regulatory RNA GlmY/phosphoribosylformylglycinamide synthetase |
| ? | NC_000913 | = 2691349 | 132 (1.210) | intergenic (‑9/+307) | glmY/purL | small regulatory RNA GlmY/phosphoribosylformylglycinamide synthetase | |||||
| * | ? | NC_000913 | = 959465 | 88 (0.800) | 9 (0.080) | 8/598 | 8.4 | 9.3% | coding (654/1284 nt) | aroA | 3‑phosphoshikimate 1‑carboxyvinyltransferase |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 9 (0.080) | 8/594 | 8.4 | 7.3% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 791973 | 115 (1.050) | coding (83/1017 nt) | galE | UDP‑glucose 4‑epimerase | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 7 (0.060) | 7/596 | 8.8 | 7.0% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2318101 | 93 (0.850) | coding (1776/2850 nt) | rcsC | histidine kinase RcsC | |||||
| * | ? | NC_000913 | = 1651548 | NA (NA) | 8 (0.070) | 6/596 | 9.3 | 6.5% | noncoding (706/706 nt) | IS2 | repeat region |
| ? | NC_000913 | 1655705 = | 116 (1.060) | intergenic (‑32/‑103) | ynfA/ynfB | putative transporter YnfA/DUF1283 domain‑containing protein YnfB | |||||