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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 218,269 | +C | coding (1042/1056 nt) | llmg_0227 → | putative membrane protein |
| RA | 295,026 | T→C | S40P (TCG→CCG) | rimI2 → | Ribosomal‑protein‑alanine acetyltransferase |
| RA | 311,626 | T→C | C179R (TGC→CGC) | lmrC → | multidrug resistance protein C |
| RA | 447,854 | G→A | A98T (GCT→ACT) | llmg_0454 → | putative beta‑glucosides‑specific IIBC component |
| RA | 549,527 | (T)6→7 | intergenic (‑197/‑190) | tnp905 ← / → tdk | transposase for insertion sequence element IS905B/Tdk protein |
| RA | 589,181 | +C | intergenic (+35/+231) | llmg_0600 → / ← llmg_0601 | glycosyl transferase/putative secreted protein |
| RA | 594,325 | T→A | I263K (ATA→AAA) | recJ → | single strand DNA‑specific exonuclease |
| RA | 617,310 | A→C | S8S (TCA→TCC) | llmg_0628 → | divalent cation transport‑related protein |
| RA | 636,592 | (A)7→6 | coding (297/1164 nt) | llmg_0642 ← | putative membrane protein |
| RA | 672,541 | A→T | L159L (CTA→CTT) | llmg_0681 → | putative membrane protein |
| RA | 674,848 | Δ1 bp | intergenic (+56/‑28) | llmg_0683 → / → llmg_pseudo_19 | putative transposase helper protein for IS712B/pseudogene |
| RA | 732,731 | +C | coding (210/975 nt) | malR → | putative maltose operon transcriptional repressor, LacI family |
| RA | 827,811 | C→T | intergenic (+153/‑32) | uxuA → / → uxuT | D‑mannonate hydrolase/Na‑galactoside symporter |
| RA | 876,869 | C→G | H82D (CAT→GAT) | amtB → | ammonium transporter AmtB |
| RA | 894,627 | +G | coding (1044/1062 nt) | llmg_0924 → | conserved hypothetical protein |
| RA | 912,618 | T→A | L46Q (CTA→CAA) | llmg_0944 → | putative secreted protein |
| RA | 912,718 | T→A | N79K (AAT→AAA) | llmg_0944 → | putative secreted protein |
| RA | 945,239 | +C | pseudogene (229/761 nt) | tnp904 → | pseudogene |
| RA | 970,845 | C→A | A78D (GCT→GAT) | llmg_1005 → | sugar kinase and transcriptional regulator |
| RA | 977,528 | Δ1 bp | coding (1177/1197 nt) | lplA → | sugar ABC transporter substrate‑binding protein |
| RA | 1,007,288 | C→T | F230F (TTC→TTT) | bglP → | similar to PTS system, beta‑glucosides specific enzyme IIABC |
| RA | 1,061,785 | A→T | I36N (ATT→AAT) | llmg_1101 ← | putative secreted protein |
| RA | 1,081,502 | A→T | K195N (AAA→AAT) | ldh → | L‑lactate dehydrogenase |
| RA | 1,093,299 | +C | coding (3979/4050 nt) | llmg_1127 → | cell wall surface anchor family protein |
| RA | 1,093,562 | +C | coding (175/246 nt) | llmg_1128 → | hypothetical protein predicted by Glimmer/Critica |
| RA | 1,201,775 | (T)8→7 | intergenic (+113/+2) | llmg_1230 → / ← tnp1077 | hypothetical protein predicted by Glimmer/Critica/pseudogene |
| RA | 1,210,283 | (A)5→6 | pseudogene (515/1046 nt) | llmg_pseudo_39 ← | pseudogene |
| RA | 1,223,555 | Δ1 bp | intergenic (+243/+302) | llmg_1251 → / ← llmg_1252 | hypothetical protein predicted by Glimmer/Critica/conserved hypothetical protein |
| RA | 1,223,557 | 2 bp→AG | intergenic (+245/+299) | llmg_1251 → / ← llmg_1252 | hypothetical protein predicted by Glimmer/Critica/conserved hypothetical protein |
| RA | 1,277,684 | T→A | N231I (AAT→ATT) | llmg_1306 ← | conserved hypothetical protein |
| RA | 1,318,548 | (A)7→6 | coding (34/348 nt) | llmg_1344 → | hypothetical protein predicted by Glimmer/Critica |
| RA | 1,492,365 | T→A | L262L (CTA→CTT) | kinE ← | sensor kinase protein |
| RA | 1,500,910 | C→A | D66E (GAC→GAA) | llmg_1528 → | hypothetical protein predicted by Glimmer/Critica |
| RA | 1,532,424 | G→C | P159R (CCC→CGC) | llmg_1560 ← | stress induced DNA binding protein (putative) |
| RA | 1,572,256 | T→A | intergenic (+54/+183) | llmg_1598 → / ← deoD | putative secreted protein/DeoD protein |
| RA | 1,572,258 | G→A | intergenic (+56/+181) | llmg_1598 → / ← deoD | putative secreted protein/DeoD protein |
| RA | 1,588,193 | T→G | Q297P (CAA→CCA) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 1,588,245 | 2 bp→AT | coding (837‑838/1170 nt) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 1,588,356 | T→A | N243Y (AAT→TAT) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 1,610,761 | T→C | I430V (ATT→GTT) | llmg_1634 ← | putative membrane protein |
| RA | 1,614,130 | +T | coding (1149/1278 nt) | mleP ← | malate transporter |
| RA | 1,655,780 | G→A | L69F (CTT→TTT) | ftsL ← | cell division protein |
| RA | 1,681,037 | T→C | E332G (GAA→GGA) | pepV ← | Dipeptidase |
| RA | 1,731,090 | T→C | G335G (GGA→GGG) | llmg_1749 ← | putative membrane protein |
| RA | 1,783,142 | G→A | A603V (GCA→GTA) | llmg_1803 ← | putative secreted protein |
| RA | 1,817,902 | C→A | E463D (GAG→GAT) | xylS ← | alpha‑xylosidase |
| RA | 1,826,407 | A→G | Y12Y (TAT→TAC) | llmg_1845 ← | metal‑dependent hydrolase |
| RA | 1,826,465 | (T)6→7 | intergenic (‑23/+300) | llmg_1845 ← / ← cspB | metal‑dependent hydrolase/cold shock‑like protein cspB |
| RA | 1,838,903 | T→C | T74A (ACT→GCT) | rmaB ← | transcriptional regulator, MarR family |
| RA | 1,853,472 | C→A | M85I (ATG→ATT) | glgP ← | glycogen phosphorylase |
| RA | 1,854,998 | T→A | V95V (GTA→GTT) | glgA ← | GlgA protein |
| RA | 1,891,450 | C→A | W87L (TGG→TTG) | llmg_1911 ← | conserved hypothetical protein |
| RA | 1,916,379 | Δ1 bp | pseudogene (355/598 nt) | llmg_pseudo_59 ← | pseudogene |
| RA | 1,921,435 | Δ1 bp | coding (76/660 nt) | llmg_1941 ← | conserved hypothetical protein |
| RA | 1,921,462 | Δ1 bp | coding (49/660 nt) | llmg_1941 ← | conserved hypothetical protein |
| RA | 1,921,474 | Δ1 bp | coding (37/660 nt) | llmg_1941 ← | conserved hypothetical protein |
| RA | 1,921,516 | C→T | intergenic (‑6/‑379) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,531 | Δ1 bp | intergenic (‑21/‑364) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,639 | Δ1 bp | intergenic (‑129/‑256) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,652 | Δ1 bp | intergenic (‑142/‑243) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,656 | Δ1 bp | intergenic (‑146/‑239) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,665 | Δ1 bp | intergenic (‑155/‑230) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,675 | Δ1 bp | intergenic (‑165/‑220) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,682 | Δ1 bp | intergenic (‑172/‑213) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,694 | Δ1 bp | intergenic (‑184/‑201) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,704 | Δ1 bp | intergenic (‑194/‑191) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,708 | Δ1 bp | intergenic (‑198/‑187) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,719 | Δ1 bp | intergenic (‑209/‑176) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,725 | Δ1 bp | intergenic (‑215/‑170) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,747 | (T)5→4 | intergenic (‑237/‑148) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,755 | Δ1 bp | intergenic (‑245/‑140) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,777 | Δ1 bp | intergenic (‑267/‑118) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,921,790 | Δ1 bp | intergenic (‑280/‑105) | llmg_1941 ← / → glnP | conserved hypothetical protein/glutamine ABC transporter permease and substrate binding protein |
| RA | 1,933,214 | 2 bp→CG | coding (224‑225/714 nt) | atpB ← | ATP synthase F0, A subunit |
| RA | 1,935,405 | (T)7→6 | pseudogene (1748/2210 nt) | comEC ← | pseudogene |
| RA | 1,942,432 | T→C | I80V (ATC→GTC) | llmg_1960 ← | hypothetical protein predicted by Glimmer/Critica |
| RA | 1,942,730 | C→A | intergenic (‑61/+328) | llmg_1960 ← / ← tenA | hypothetical protein predicted by Glimmer/Critica/transcriptional activator TenA |
| RA | 2,044,751 | G→A | A37V (GCA→GTA) | ftsA ← | cell division protein ftsA |
| RA | 2,112,674 | +T | intergenic (‑79/+54) | llmg_2151 ← / ← llmg_2152 | Hypothetical protein ycaQ/Hypothetical protein ycaQ |
| RA | 2,122,554 | G→A | S58L (TCG→TTG) | cfa ← | cyclopropane‑fatty‑acyl‑phospholipid synthase |
| RA | 2,122,558 | C→T | A57T (GCC→ACC) | cfa ← | cyclopropane‑fatty‑acyl‑phospholipid synthase |
| RA | 2,183,058 | (A)5→4 | coding (399/1161 nt) | llmg_2218 ← | predicted transcriptional regulator |
| RA | 2,230,259 | Δ1 bp | coding (1758/1779 nt) | llmg_2272 ← | conserved hypothetical protein |
| RA | 2,266,724 | T→C | I10T (ATT→ACT) | argR → | arginine repressor |
| RA | 2,492,912 | G→A | A203V (GCA→GTA) | gapB ← | glyceraldehyde 3‑phosphate dehydrogenase |
| RA | 2,510,293 | Δ1 bp | coding (777/816 nt) | purR ← | pur operon repressor |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AM406671 | 1583930 = | NA (NA) | 1020 (0.960) | 249/294 | 1.0 | NA | intergenic (‑98/‑80) | glf2/tnp712 | pseudogene/transposase for insertion sequence element IS712G |
| ? | AM406671 | 1632643 = | NA (NA) | coding (132/261 nt) | llmg_1655 | conserved hypothetical protein | |||||
| * | ? | AM406671 | 2086138 = | NA (NA) | 1315 (1.230) | 283/296 | 0.0 | 95.0% | intergenic (‑41/+48) | ps442/tnp905 | putative terminase large subunit/pseudogene |
| ? | AM406671 | = 2090433 | 69 (0.060) | coding (31/309 nt) | ps435 | hypothetical protein predicted by Glimmer/Critica | |||||
| * | ? | AM406671 | = 2087450 | NA (NA) | 1270 (1.190) | 286/296 | 0.0 | 94.7% | intergenic (‑89/+270) | tnp905/ps440 | pseudogene/phage terminase small subunit |
| ? | AM406671 | 2090426 = | 71 (0.070) | coding (38/309 nt) | ps435 | hypothetical protein predicted by Glimmer/Critica | |||||