mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 26,455 | T→C | intergenic (+111/‑39) | LLMG_RS00135 → / → LLMG_RS00140 | tRNA‑Asn/PTS transporter subunit EIIC |
| RA | 187,916 | C→T | G20R (GGA→AGA) | LLMG_RS01045 ← | type II CAAX endopeptidase family protein |
| RA | 218,269 | +C | coding (1042/1056 nt) | LLMG_RS01195 → | DUF2142 domain‑containing protein |
| RA | 311,626 | T→C | C173R (TGC→CGC) | lmrC → | multidrug efflux ABC transporter LmrCD subunit C |
| MC JC | 384,965 | 533 bp→5 bp | coding (205‑737/945 nt) | LLMG_RS02010 ← | L‑lactate dehydrogenase |
| RA | 404,128 | T→G | intergenic (+83/‑4) | groES → / → groL | co‑chaperone GroES/chaperonin GroEL |
| RA | 430,174 | C→T | intergenic (+196/‑97) | LLMG_RS02235 → / → LLMG_RS02240 | MurR/RpiR family transcriptional regulator/PTS sugar transporter subunit IIC |
| RA | 430,179 | T→G | intergenic (+201/‑92) | LLMG_RS02235 → / → LLMG_RS02240 | MurR/RpiR family transcriptional regulator/PTS sugar transporter subunit IIC |
| RA | 549,527 | (T)6→7 | intergenic (‑197/‑190) | LLMG_RS02885 ← / → LLMG_RS02890 | IS256‑like element IS905 family transposase/thymidine kinase |
| RA | 589,181 | +C | intergenic (+35/+231) | LLMG_RS03120 → / ← LLMG_RS03125 | glycosyltransferase family 2 protein/hypothetical protein |
| RA | 594,325 | T→A | I263K (ATA→AAA) | recJ → | single‑stranded‑DNA‑specific exonuclease RecJ |
| RA | 617,310 | A→C | S8S (TCA→TCC) | LLMG_RS03280 → | magnesium transporter CorA family protein |
| RA | 636,592 | (A)7→6 | coding (297/1164 nt) | LLMG_RS03345 ← | ABC transporter permease |
| RA | 672,541 | A→T | L159L (CTA→CTT) | LLMG_RS03545 → | helix‑turn‑helix transcriptional regulator |
| RA | 672,705 | T→G | pseudogene (119/138 nt) | LLMG_RS13115 → | transposase |
| MC JC | 752,091 | Δ985 bp | [pta] | [pta] | |
| RA | 876,869 | C→G | H82D (CAT→GAT) | LLMG_RS04645 → | ammonium transporter |
| RA | 894,627 | +G | coding (1044/1062 nt) | LLMG_RS04715 → | DUF916 and DUF3324 domain‑containing protein |
| RA | 912,618 | T→A | L46Q (CTA→CAA) | LLMG_RS04815 → | hypothetical protein |
| RA | 912,718 | T→A | N79K (AAT→AAA) | LLMG_RS04815 → | hypothetical protein |
| RA | 945,239 | +C | pseudogene (615/1147 nt) | LLMG_RS13415 → | IS3 family transposase |
| RA | 977,528 | Δ1 bp | coding (1177/1197 nt) | LLMG_RS05140 → | extracellular solute‑binding protein |
| RA | 1,007,288 | C→T | F230F (TTC→TTT) | LLMG_RS05310 → | beta‑glucoside‑specific PTS transporter subunit IIABC |
| RA | 1,061,785 | A→T | I36N (ATT→AAT) | LLMG_RS05590 ← | TPM domain‑containing protein |
| MC JC | 1,081,159 | 35 bp→8 bp | coding (242‑276/978 nt) | LLMG_RS05690 → | L‑lactate dehydrogenase |
| RA | 1,093,299 | +C | coding (3979/4050 nt) | LLMG_RS13005 → | Ig‑like domain‑containing protein |
| RA | 1,093,562 | +C | pseudogene (205/276 nt) | LLMG_RS13840 → | hypothetical protein |
| RA | 1,167,414 | T→G | intergenic (+64/‑55) | LLMG_RS06065 → / → LLMG_RS06070 | hypothetical protein/trypsin‑like peptidase domain‑containing protein |
| RA | 1,210,283 | (A)5→6 | coding (515/525 nt) | LLMG_RS13870 ← | LacI family DNA‑binding transcriptional regulator |
| RA | 1,223,555 | Δ1 bp | intergenic (+243/+302) | LLMG_RS06320 → / ← LLMG_RS06325 | hypothetical protein/MerR family transcriptional regulator |
| RA | 1,223,557 | 2 bp→AG | intergenic (+245/+299) | LLMG_RS06320 → / ← LLMG_RS06325 | hypothetical protein/MerR family transcriptional regulator |
| RA | 1,277,684 | T→A | N231I (AAT→ATT) | LLMG_RS06625 ← | Cna B‑type domain‑containing protein |
| RA | 1,318,548 | (A)7→6 | coding (98/162 nt) | LLMG_RS13880 → | hypothetical protein |
| MC JC | 1,397,012 | 512 bp→5 bp | coding (215‑726/972 nt) | LLMG_RS07210 ← | L‑lactate dehydrogenase |
| RA | 1,492,365 | T→A | L262L (CTA→CTT) | LLMG_RS07640 ← | ATP‑binding protein |
| RA | 1,500,910 | C→A | D145E (GAC→GAA) | LLMG_RS13905 → | WYL domain‑containing protein |
| RA | 1,532,424 | G→C | P159R (CCC→CGC) | LLMG_RS07840 ← | hypothetical protein |
| RA | 1,572,256 | T→A | intergenic (+54/+183) | LLMG_RS08045 → / ← deoD | hypothetical protein/purine‑nucleoside phosphorylase |
| RA | 1,572,258 | G→A | intergenic (+56/+181) | LLMG_RS08045 → / ← deoD | hypothetical protein/purine‑nucleoside phosphorylase |
| RA | 1,588,193 | T→G | Q297P (CAA→CCA) | LLMG_RS08135 ← | nucleotide sugar dehydrogenase |
| RA | 1,588,245 | 2 bp→AT | coding (837‑838/1170 nt) | LLMG_RS08135 ← | nucleotide sugar dehydrogenase |
| RA | 1,588,356 | T→A | N243Y (AAT→TAT) | LLMG_RS08135 ← | nucleotide sugar dehydrogenase |
| RA | 1,610,761 | T→C | I430V (ATT→GTT) | LLMG_RS08230 ← | hypothetical protein |
| RA | 1,614,130 | +T | coding (1149/1278 nt) | LLMG_RS08245 ← | citrate:cation symporter |
| RA | 1,660,056 | (T)7→8 | intergenic (‑602/+100) | LLMG_RS08470 ← / ← recN | TMEM175 family protein/DNA repair protein RecN |
| RA | 1,681,037 | T→C | E332G (GAA→GGA) | pepV ← | dipeptidase PepV |
| RA | 1,731,090 | T→C | G335G (GGA→GGG) | LLMG_RS08790 ← | YibE/F family protein |
| RA | 1,826,407 | A→G | Y12Y (TAT→TAC) | LLMG_RS09240 ← | MBL fold metallo‑hydrolase |
| RA | 1,826,465 | (T)6→7 | intergenic (‑23/+300) | LLMG_RS09240 ← / ← LLMG_RS09245 | MBL fold metallo‑hydrolase/cold‑shock protein |
| RA | 1,838,903 | T→C | T74A (ACT→GCT) | LLMG_RS09315 ← | MarR family transcriptional regulator |
| RA | 1,853,472 | C→A | M85I (ATG→ATT) | LLMG_RS09365 ← | glycogen/starch/alpha‑glucan phosphorylase |
| RA | 1,854,998 | T→A | V85V (GTA→GTT) | glgA ← | glycogen synthase GlgA |
| RA | 1,887,895 | G→T | L533I (CTA→ATA) | pepF ← | oligoendopeptidase F |
| RA | 1,891,450 | C→A | W87L (TGG→TTG) | LLMG_RS09565 ← | YdcF family protein |
| RA | 1,916,379 | Δ1 bp | pseudogene (355/598 nt) | LLMG_RS09685 ← | HAD family hydrolase |
| RA | 1,921,435 | Δ1 bp | coding (76/660 nt) | LLMG_RS09710 ← | VTT domain‑containing protein |
| RA | 1,921,462 | Δ1 bp | coding (49/660 nt) | LLMG_RS09710 ← | VTT domain‑containing protein |
| RA | 1,921,474 | Δ1 bp | coding (37/660 nt) | LLMG_RS09710 ← | VTT domain‑containing protein |
| RA | 1,921,516 | C→T | intergenic (‑6/‑379) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,531 | Δ1 bp | intergenic (‑21/‑364) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,639 | Δ1 bp | intergenic (‑129/‑256) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,652 | Δ1 bp | intergenic (‑142/‑243) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,656 | Δ1 bp | intergenic (‑146/‑239) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,665 | Δ1 bp | intergenic (‑155/‑230) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,675 | Δ1 bp | intergenic (‑165/‑220) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,682 | Δ1 bp | intergenic (‑172/‑213) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,694 | Δ1 bp | intergenic (‑184/‑201) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,704 | Δ1 bp | intergenic (‑194/‑191) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,708 | Δ1 bp | intergenic (‑198/‑187) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,719 | Δ1 bp | intergenic (‑209/‑176) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,725 | Δ1 bp | intergenic (‑215/‑170) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,747 | (T)5→4 | intergenic (‑237/‑148) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,755 | Δ1 bp | intergenic (‑245/‑140) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,777 | Δ1 bp | intergenic (‑267/‑118) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,921,790 | Δ1 bp | intergenic (‑280/‑105) | LLMG_RS09710 ← / → LLMG_RS09715 | VTT domain‑containing protein/amino acid ABC transporter substrate‑binding protein/permease |
| RA | 1,933,214 | 2 bp→CG | coding (224‑225/714 nt) | atpB ← | F0F1 ATP synthase subunit A |
| RA | 1,935,405 | (T)7→6 | pseudogene (1748/2210 nt) | LLMG_RS09775 ← | DNA internalization‑related competence protein ComEC/Rec2 |
| RA | 1,942,432 | T→C | I80V (ATC→GTC) | LLMG_RS09805 ← | SLC13 family permease |
| RA | 1,942,730 | C→A | intergenic (‑61/+328) | LLMG_RS09805 ← / ← tenA | SLC13 family permease/thiaminase II |
| RA | 2,026,794 | T→G | E596A (GAA→GCA) | pnp ← | polyribonucleotide nucleotidyltransferase |
| RA | 2,112,674 | +T | pseudogene (303/1128 nt) | LLMG_RS10765 ← | winged helix DNA‑binding domain‑containing protein |
| RA | 2,122,554 | G→A | S58L (TCG→TTG) | LLMG_RS10800 ← | cyclopropane‑fatty‑acyl‑phospholipid synthase family protein |
| RA | 2,122,558 | C→T | A57T (GCC→ACC) | LLMG_RS10800 ← | cyclopropane‑fatty‑acyl‑phospholipid synthase family protein |
| RA | 2,183,058 | (A)5→4 | coding (399/1161 nt) | LLMG_RS11130 ← | Rgg/GadR/MutR family transcriptional regulator |
| RA | 2,230,259 | Δ1 bp | coding (1758/1779 nt) | LLMG_RS11405 ← | glycerophosphodiester phosphodiesterase |
| RA | 2,383,055 | Δ1 bp | intergenic (+245/‑10) | LLMG_RS12210 → / → adhE | lactonase family protein/bifunctional acetaldehyde‑CoA/alcohol dehydrogenase |
| MC JC | 2,383,067 | Δ2,719 bp | [adhE] | [adhE] | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_009004 | 669805 | 671337–670201 | 397–1533 | 582 [1] | [220] 228 | LLMG_RS03520–[LLMG_RS13110] | LLMG_RS03520,[LLMG_RS13110] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_009004 | = 669804 | 1 (0.000) | 578 (0.860) | 232/294 | 0.6 | 99.8% | intergenic (‑59/‑271) | LLMG_RS03515/LLMG_RS03520 | GNAT family N‑acetyltransferase/hypothetical protein |
| ? | NC_009004 | = 675922 | NA (NA) | intergenic (+55/‑633) | LLMG_RS03560/LLMG_RS13605 | IS3 family transposase/hypothetical protein | |||||
| * | ? | NC_009004 | 1298894 = | NA (NA) | 598 (0.890) | 230/294 | 0.6 | 54.9% | coding (329/342 nt) | LLMG_RS06700 | AraC family ligand binding domain‑containing protein |
| ? | NC_009004 | = 1615073 | 491 (0.730) | coding (206/1278 nt) | LLMG_RS08245 | citrate:cation symporter | |||||
| * | ? | NC_009004 | 1298894 = | NA (NA) | 9124 (13.520) | 292/294 | 0.0 | 99.7% | coding (329/342 nt) | LLMG_RS06700 | AraC family ligand binding domain‑containing protein |
| ? | NC_009004 | = 1621394 | 31 (0.050) | intergenic (‑102/+106) | LLMG_RS08265/LLMG_RS08270 | 2,3‑butanediol dehydrogenase/FtsW/RodA/SpoVE family cell cycle protein | |||||
| * | ? | NC_009004 | = 1586092 | NA (NA) | 647 (0.970) | 190/292 | 1.8 | NA | coding (726/774 nt) | LLMG_RS08120 | hypothetical protein |
| ? | NC_009004 | = 1632647 | NA (NA) | coding (128/217 nt) | LLMG_RS08320 | IS3‑like element IS981 family transposase | |||||
| * | ? | NC_009004 | 1615066 = | 29 (0.040) | 9792 (14.510) | 292/294 | 0.0 | 99.7% | coding (213/1278 nt) | LLMG_RS08245 | citrate:cation symporter |
| ? | NC_009004 | 1646630 = | NA (NA) | intergenic (‑104/‑89) | LLMG_RS08410/LLMG_RS08415 | GTP pyrophosphokinase family protein/IS256‑like element IS905 family transposase | |||||
| * | ? | NC_009004 | 1621387 = | 465 (0.690) | 683 (1.010) | 249/294 | 0.2 | 59.5% | intergenic (‑95/+113) | LLMG_RS08265/LLMG_RS08270 | 2,3‑butanediol dehydrogenase/FtsW/RodA/SpoVE family cell cycle protein |
| ? | NC_009004 | 1859127 = | NA (NA) | coding (38/1458 nt) | LLMG_RS09385 | 4‑alpha‑glucanotransferase | |||||