mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 572,216 | C→T | 30.8% | pseudogene (66/1040 nt) | nmpC ← | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 764,350 | T→C | 44.4% | L306P (CTG→CCG) | mngB → | alpha‑mannosidase |
| RA | 882,839 | T→C | 21.2% | intergenic (‑44/‑40) | ybjJ ← / → rcdA | putative transporter/transcriptional regulator of csgD and ybiJI; autoregulator |
| RA | 2,051,591 | G→T | 69.1% | intergenic (‑8/+93) | asnW ← / ← yeeO | tRNA‑Asn/putative multdrug exporter, MATE family |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 87.2% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,420,353 | A→C | 75.1% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 54.3% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,178,277 | G→T | 42.1% | E27* (GAA→TAA) | yqiC → | BMFP family putative fusogenic protein |
| RA | 4,050,838 | A→T | 59.8% | V186E (GTA→GAA) | glnA ← | glutamine synthetase |
| RA | 4,546,084 | G→T | 53.6% | H18Q (CAC→CAA) | yjiC ← | uncharacterized protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 881400 | 881433 | 34 | 2 [1] | [0] 2 | ybjI | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis |
| * | * | ÷ | CP009273 | 2084775 | 2084822 | 48 | 2 [1] | [0] 2 | hisD | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| * | * | ÷ | CP009273 | 2084973 | 2085072 | 100 | 2 [0] | [1] 2 | hisD | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| * | * | ÷ | CP009273 | 4051946 | 4051982 | 37 | 2 [1] | [1] 2 | typA | GTP‑binding protein |
| * | * | ÷ | CP009273 | 4436804 | 4436812 | 9 | 2 [1] | [1] 2 | tamB | translocation and assembly module for autotransporter export, inner membrane subunit |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 287112 | NA (NA) | 5 (0.350) | 5/274 | NT | 55.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | CP009273 | = 1973068 | 4 (0.280) | intergenic (‑614/‑166) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 21 (1.460) | 17/274 | NT | 55.3% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | 17 (1.180) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 376716 = | NA (NA) | 6 (0.420) | 5/274 | NT | 60.0% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
| ? | CP009273 | 559695 = | 4 (0.280) | coding (242/633 nt) | sfmZ | response regulator family protein | |||||
| * | ? | CP009273 | = 378045 | NA (NA) | 10 (0.700) | 10/272 | NT | 66.8% | intergenic (+10/+2) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
| ? | CP009273 | = 559700 | 5 (0.350) | coding (237/633 nt) | sfmZ | response regulator family protein | |||||
| * | ? | CP009273 | 1203246 = | 2 (0.140) | 6 (0.470) | 6/242 | NT | 60.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 6 (0.470) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 2 (0.140) | 7 (0.550) | 5/242 | NT | 64.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 6 (0.470) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1973060 = | 5 (0.350) | 4 (0.280) | 4/274 | NT | 44.4% | intergenic (‑606/‑174) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | 2399187 = | 11 (0.760) | 5 (0.350) | 5/274 | NT | 31.2% | coding (934/939 nt) | lrhA | transcriptional repressor of flagellar, motility and chemotaxis genes |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2455548 | 25 (1.730) | 6 (0.420) | 6/272 | NT | 19.5% | coding (764/1341 nt) | fadL | long‑chain fatty acid outer membrane transporter |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||