mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 109,553 | T→C | 7.4% | Y599Y (TAT→TAC) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamin‑binding |
| RA | 204,511 | C→T | 100% | intergenic (+111/‑73) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 204,556 | A→G | 100% | intergenic (+156/‑28) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 214,925 | A→C | 70.7% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 214,931 | A→C | 74.4% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 348,496 | A→C | 5.2% | N265T (AAC→ACC) | gcl → | glyoxylate carboligase |
| RA | 348,499 | C→T | 5.2% | A266V (GCA→GTA) | gcl → | glyoxylate carboligase |
| RA | 394,053 | T→C | 7.0% | V71A (GTA→GCA) | ahpC → | alkyl hydroperoxide reductase, C22 subunit |
| RA | 755,969 | C→G | 8.4% | V32V (GTC→GTG) | lolD → | outer membrane‑specific lipoprotein transporter subunit |
| RA | 954,077 | T→C | 6.4% | M506V (ATG→GTG) | gadC ← | predicted glutamate:gamma‑aminobutyric acid antiporter |
| RA | 954,082 | A→C | 5.4% | I504S (ATT→AGT) | gadC ← | predicted glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,036,505 | G→A | 100% | A632A (GCG→GCA) | rsxC → | fused predicted 4Fe‑4S ferredoxin‑type protein |
| RA | 1,692,652 | A→G | 10.3% | I108I (ATT→ATC) | iscU ← | scaffold protein |
| RA | 1,692,655 | A→C | 10.3% | S107S (TCT→TCG) | iscU ← | scaffold protein |
| RA | 1,692,658 | A→G | 11.5% | C106C (TGT→TGC) | iscU ← | scaffold protein |
| RA | 1,692,667 | T→C | 12.5% | K103K (AAA→AAG) | iscU ← | scaffold protein |
| RA | 1,692,670 | C→G | 12.5% | V102V (GTG→GTC) | iscU ← | scaffold protein |
| RA | 1,763,540 | A→G | 6.7% | noncoding (304/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,556 | T→C | 42.9% | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,558 | G→C | 25.0% | noncoding (286/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,559 | G→T | 14.0% | noncoding (285/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,580 | G→T | 16.5% | noncoding (264/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,594 | A→T | 10.9% | noncoding (250/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,636 | A→G | 35.4% | noncoding (208/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,804,090 | G→A | 76.4% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 1,816,284 | T→C | 10.0% | K217K (AAA→AAG) | recA ← | DNA strand exchange and recombination protein with protease and nuclease activity |
| RA | 1,816,290 | C→T | 10.0% | A215A (GCG→GCA) | recA ← | DNA strand exchange and recombination protein with protease and nuclease activity |
| RA | 1,892,019:1 | +GC | 100% | intergenic (‑437/+54) | gudP ← / ← ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| RA | 1,910,405 | C→T | 6.4% | V117M (GTG→ATG) | ppdB ← | conserved hypothetical protein |
| RA | 2,086,490 | C→A | 9.2% | P89T (CCG→ACG) | yqjG → | predicted S‑transferase |
| RA | 2,102,851 | G→A | 8.6% | W143* (TGG→TAG) | yhaV → | conserved hypothetical protein |
| RA | 2,254,620 | G→A | 12.3% | D806D (GAC→GAT) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,254,623 | C→T | 12.0% | Q805Q (CAG→CAA) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,254,628 | C→T | 12.6% | A804T (GCG→ACG) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,254,635 | A→C | 9.8% | V801V (GTT→GTG) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,254,647 | A→G | 13.5% | T797T (ACT→ACC) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,255,098 | G→A | 7.7% | P647L (CCG→CTG) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,336,250 | T→C | 5.9% | G212G (GGT→GGC) | fdoH → | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 2,359,867 | G→A | 38.0% | noncoding (1228/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,876 | C→T | 34.1% | noncoding (1219/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,469,879 | A→G | 13.1% | K287K (AAA→AAG) | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,881 | C→A | 12.6% | T288N (ACT→AAT) ‡ | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,882 | T→A | 12.4% | T288T (ACT→ACA) ‡ | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,885 | T→C | 12.5% | G289G (GGT→GGC) | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,888 | T→G | 15.2% | S290S (TCT→TCG) | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,897 | C→G | 16.6% | S293S (TCC→TCG) | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,898 | G→A | 15.8% | V294I (GTA→ATA) ‡ | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,900 | A→C | 16.2% | V294V (GTA→GTC) ‡ | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,469,906 | A→C | 17.6% | A296A (GCA→GCC) | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,543,240 | T→A | 10.4% | intergenic (+4/+28) | rfaK → / ← rfaL | lipopolysaccharide core biosynthesis/O‑antigen ligase |
| RA | 2,543,241 | T→A | 10.5% | intergenic (+5/+27) | rfaK → / ← rfaL | lipopolysaccharide core biosynthesis/O‑antigen ligase |
| RA | 2,682,335 | T→C | 11.6% | K459K (AAA→AAG) | yhgF ← | predicted transcriptional accessory protein |
| RA | 2,781,131 | T→C | 12.7% | N702N (AAT→AAC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 2,781,132 | G→A | 12.7% | V703M (GTG→ATG) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 2,781,149 | T→C | 8.7% | F708F (TTT→TTC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 2,781,153 | G→C | 7.8% | E710Q (GAA→CAA) ‡ | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 2,781,155 | A→G | 8.2% | E710E (GAA→GAG) ‡ | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 2,781,158 | G→C | 7.5% | G711G (GGG→GGC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 2,781,161 | A→G | 7.7% | K712K (AAA→AAG) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 2,811,198 | A→C | 8.2% | S516S (TCT→TCG) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,811,228 | A→G | 7.1% | V506V (GTT→GTC) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,811,239 | C→A | 6.9% | A503S (GCG→TCG) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,811,428 | T→C | 6.5% | M440V (ATG→GTG) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,923,265 | G→T | 12.5% | L653M (CTG→ATG) | valS ← | valyl‑tRNA synthetase |
| RA | 2,923,269 | A→G | 11.9% | F651F (TTT→TTC) | valS ← | valyl‑tRNA synthetase |
| RA | 2,923,276 | C→G | 12.1% | S649T (AGC→ACC) | valS ← | valyl‑tRNA synthetase |
| RA | 2,923,278 | G→C | 12.0% | A648A (GCC→GCG) | valS ← | valyl‑tRNA synthetase |
| RA | 2,923,281 | G→A | 12.5% | N647N (AAC→AAT) | valS ← | valyl‑tRNA synthetase |
| RA | 2,923,296 | A→G | 11.9% | C642C (TGT→TGC) | valS ← | valyl‑tRNA synthetase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | Exported | 252003 | 252056 | 54 | 11 [6] | [9] 11 | malZ | maltodextrin glucosidase |
| * | * | ÷ | Exported | 1847541 | 1847671 | 131 | 11 [10] | [10] 11 | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein |
| * | * | ÷ | Exported | 1945283 | 1945340 | 58 | 15 [8] | [10] 12 | ygfF/gcvP | predicted NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | Exported | 204714 = | NA (NA) | 6 (0.130) | 3/86 | NT | NA | noncoding (131/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | Exported | 204732 = | NA (NA) | noncoding (149/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | Exported | = 215622 | 27 (0.500) | 69 (2.800) +27 bp |
27/46 | NT | 79.8% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | Exported | 2705182 = | 49 (0.910) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | Exported | 436259 = | 39 (0.730) | 75 (1.520) | 44/92 | NT | 71.1% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | Exported | = 2706018 | 25 (0.510) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | Exported | = 436833 | 87 (1.620) | 118 (2.200) | 47/100 | NT | 61.6% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | Exported | 1803907 = | 60 (1.120) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | Exported | = 708201 | 55 (1.030) | 5 (0.100) | 3/90 | NT | 9.7% | coding (567/1053 nt) | yceA | conserved hypothetical protein |
| ? | Exported | = 708230 | 44 (0.910) | coding (596/1053 nt) | yceA | conserved hypothetical protein | |||||
| * | ? | Exported | 778349 = | 62 (1.160) | 15 (0.340) | 4/82 | NT | 25.2% | intergenic (‑55/‑465) | minC/ycgJ | cell division inhibitor/hypothetical protein |
| ? | Exported | 778373 = | 38 (0.860) | intergenic (‑79/‑441) | minC/ycgJ | cell division inhibitor/hypothetical protein | |||||
| * | ? | Exported | 839554 = | 66 (1.230) | 8 (0.160) | 3/92 | NT | 9.9% | coding (750/843 nt) | purU | formyltetrahydrofolate hydrolase |
| ? | Exported | 839587 = | 85 (1.720) | coding (717/843 nt) | purU | formyltetrahydrofolate hydrolase | |||||
| * | ? | Exported | 1151063 = | 50 (0.930) | 5 (0.100) | 3/90 | NT | 11.1% | intergenic (+87/‑143) | nadE/ydjQ | NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair |
| ? | Exported | 1151083 = | 35 (0.730) | intergenic (+107/‑123) | nadE/ydjQ | NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair | |||||
| * | ? | Exported | = 1590976 | 48 (0.890) | 4 (0.080) | 3/90 | NT | 8.7% | coding (170/735 nt) | yfeS | conserved hypothetical protein |
| ? | Exported | = 1590999 | 41 (0.850) | coding (193/735 nt) | yfeS | conserved hypothetical protein | |||||
| * | ? | Exported | 1811075 = | 61 (1.140) | 9 (0.190) | 3/88 | NT | 17.4% | intergenic (‑50/+149) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | Exported | 1811475 = | 32 (0.680) | intergenic (‑36/+163) | argY/argV | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | Exported | = 1908195 | 65 (1.210) | 4 (0.080) | 3/92 | NT | 5.4% | coding (1271/3369 nt) | recC | exonuclease V (RecBCD complex), gamma chain |
| ? | Exported | = 1908209 | 79 (1.600) | coding (1257/3369 nt) | recC | exonuclease V (RecBCD complex), gamma chain | |||||
| * | ? | Exported | = 2059386 | 89 (1.660) | 8 (0.160) | 3/94 | NT | 8.7% | coding (650/1464 nt) | ygjE | predicted tartrate:succinate antiporter |
| ? | Exported | = 2059405 | 85 (1.690) | coding (669/1464 nt) | ygjE | predicted tartrate:succinate antiporter | |||||
| * | ? | Exported | = 2460619 | 31 (0.580) | 3 (0.070) | 3/86 | NT | 9.4% | intergenic (+237/‑142) | mioC/gidA | FMN‑binding protein MioC/glucose‑inhibited cell‑division protein |
| ? | Exported | = 2460630 | 31 (0.670) | intergenic (+248/‑131) | mioC/gidA | FMN‑binding protein MioC/glucose‑inhibited cell‑division protein | |||||