mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.18
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 264,278 | G→A | A420T (GCC→ACC) | iolT | transporter major facilitator superfamily MFS_1, Myo‑inositol transporter |
| RA | 615,483 | T→C | L422P (CTG→CCG) | treB | PTS system beta‑glucoside‑specific transporter subunit IIABC |
| JC | 656,565 | 3 bp x 2 | duplication | glpD | alpha‑glycerophosphate oxidase |
| RA | 751,602 | G→A | intergenic (+35/‑224) | napA/gph | Na/H antiporter/haloacid dehalogenase‑like family hydrolase |
| RA | 751,632 | 2 bp→GC | intergenic (+65/‑193) | napA/gph | Na/H antiporter/haloacid dehalogenase‑like family hydrolase |
| RA | 751,663 | T→C | intergenic (+96/‑163) | napA/gph | Na/H antiporter/haloacid dehalogenase‑like family hydrolase |
| JC | 876,402 | 3 bp x 2 | duplication | cutC | copper homeostasis protein CutC |
| RA | 1,154,682 | T→G | intergenic (‑80/+353) | LGG_01157/pepD | transporter major facilitator superfamily MFS_1/dipeptidase A |
| RA | 1,372,183 | T→A | M406M (TTG→ATG) | ycjM | 2',3'‑cyclic‑nucleotide 2'‑phosphodiesterase |
| RA | 1,873,058 | A→G | P249P (CCT→CCC) | LGG_01843 | hypothetical protein |
| RA | 1,873,063 | Δ1 bp | coding (742/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,071 | +T | coding (734/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,078 | Δ1 bp | coding (727/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,089 | G→A | A239V (GCC→GTC) | LGG_01843 | hypothetical protein |
| RA | 1,873,091 | 2 bp→CA | coding (713‑714/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,110 | C→T | S232N (AGT→AAT) | LGG_01843 | hypothetical protein |
| RA | 1,873,122 | C→T | R228H (CGC→CAC) | LGG_01843 | hypothetical protein |
| RA | 1,873,131 | +A | coding (674/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,133 | 1 bp→GG | coding (672/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,146 | 2 bp→AG | coding (658‑659/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,149 | G→C | A219G (GCG→GGG) | LGG_01843 | hypothetical protein |
| RA | 1,873,152 | C→G | S218T (AGC→ACC) | LGG_01843 | hypothetical protein |
| RA | 1,873,180 | A→G | S209P (TCA→CCA) | LGG_01843 | hypothetical protein |
| RA | 1,873,210 | T→C | S199G (AGC→GGC) | LGG_01843 | hypothetical protein |
| RA | 1,873,245 | T→A | D187V (GAT→GTT) | LGG_01843 | hypothetical protein |
| RA | 1,873,252 | 3 bp→AT | coding (551‑553/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,272 | T→C | N178S (AAC→AGC) | LGG_01843 | hypothetical protein |
| RA | 1,873,274 | C→T | L177L (CTG→CTA) | LGG_01843 | hypothetical protein |
| RA | 1,873,277 | 3 bp→GGA | coding (526‑528/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,298 | 2 bp→TG | coding (506‑507/795 nt) | LGG_01843 | hypothetical protein |
| RA | 1,873,301 | A→G | R168R (CGT→CGC) | LGG_01843 | hypothetical protein |
| RA | 1,873,847 | +C | intergenic (‑43/‑58) | LGG_01843/LGG_01844 | hypothetical protein/hypothetical protein |
| RA | 1,873,850 | 5 bp→TTATG | intergenic (‑46/‑51) | LGG_01843/LGG_01844 | hypothetical protein/hypothetical protein |
| RA | 1,873,856 | A→G | intergenic (‑52/‑49) | LGG_01843/LGG_01844 | hypothetical protein/hypothetical protein |
| MC JC | 1,877,309 | Δ1,586 bp | LGG_01848 | LGG_01848 | |
| RA | 1,883,242 | C→A | intergenic (‑292/+93) | ABC‑SBP/LGG_01854 | ABC transporter substrate‑binding protein/hypothetical protein |
| RA | 1,994,717 | T→A | D903V (GAT→GTT) | LGG_01953 | hypothetical protein |
| RA | 2,452,317 | A→G | Q43Q (CAA→CAG) | LGG_02375 | hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_013198 | 2574291–2574343 | 2574574–2574418 | 76–284 | 190 [170] | [186] 194 | [LGG_02511]–[LGG_02512] | [LGG_02511], [LGG_02512] |
| Unassigned new junction evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | annotation | gene | product | ||
| * | ? | NC_013198 | = 240672 | 12 (0.016) | 1122 (1.488) | 166/192 | 0.0 | coding (716/759 nt) | LGG_00234 | hypothetical protein |
| ? | NC_013198 | 241548 = | 4 (0.005) | intergenic (+21/‑25) | is8/LGG_00237 | transposase IS4 family protein/hypothetical protein | ||||
| * | ? | NC_013198 | = 594623 | 2 (0.003) | 604 (0.845) | 127/182 | 0.4 | intergenic (‑105/+61) | yicL/LGG_00589 | carboxylate/amino acid/amine transporter/hypothetical protein |
| ? | NC_013198 | 596210 = | 4 (0.005) | intergenic (‑123/+83) | LGG_00589/LGG_00590 | hypothetical protein/hypothetical protein | ||||
| * | ? | NC_013198 | 751569 = | 724 (1.084) | 634 (0.949) | 114/170 | 0.5 | intergenic (+2/‑257) | napA/gph | Na/H antiporter/haloacid dehalogenase‑like family hydrolase |
| ? | NC_013198 | = 751695 | 440 (0.560) | intergenic (+128/‑131) | napA/gph | Na/H antiporter/haloacid dehalogenase‑like family hydrolase | ||||
| * | ? | NC_013198 | = 1038045 | 4 (0.005) | 366 (0.490) | 104/190 | 1.2 | coding (872/978 nt) | LGG_01023 | adenine specific DNA methylase Mod |
| ? | NC_013198 | 1038906 = | 0 (0.000) | intergenic (+13/‑238) | is36/LGG_01026 | transposase IS4 family protein/type III restriction‑modification system methylation subunit | ||||
| * | ? | NC_013198 | 1058951 = | 1236 (1.605) | 416 (0.540) | 83/196 | 2.2 | coding (53/183 nt) | LGG_01046 | hypothetical protein |
| ? | NC_013198 | = 2898115 | 856 (1.090) | coding (225/237 nt) | LGG_02835 | hypothetical protein | ||||
| * | ? | NC_013198 | 1998770 = | 432 (0.573) | 974 (1.292) | 94/192 | 1.6 | intergenic (+363/‑314) | lciIC/LGG_01955 | XRE family transcriptional regulator/reverse transcriptase‑like protein |
| ? | NC_013198 | = 1998907 | 794 (1.011) | intergenic (+500/‑177) | lciIC/LGG_01955 | XRE family transcriptional regulator/reverse transcriptase‑like protein | ||||
| * | ? | NC_013198 | 2948923 = | 866 (1.395) | 1120 (1.805) | 141/158 | 0.0 | intergenic (‑229/+118) | LGG_02884/xerC | PEP phosphonomutase‑like protein/phage‑related integrase |
| ? | NC_013198 | = 2963051 | 510 (0.649) | intergenic (‑243/+7) | ytgB/tRNA‑Lys | transglycosylase‑associated protein/tRNA‑Lys | ||||