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 | 13,583 | T→G | 6.6% | V474G (GTT→GGT) | dnaK → | chaperone Hsp70, co‑chaperone with DnaJ |
| RA | 13,586 | C→A | 6.5% | T475N (ACC→AAC) | dnaK → | chaperone Hsp70, co‑chaperone with DnaJ |
| RA | 13,594 | A→C | 6.1% | I478L (ATC→CTC) | dnaK → | chaperone Hsp70, co‑chaperone with DnaJ |
| RA | 62,466 | A→G | 5.1% | Y331Y (TAT→TAC) | polB ← | DNA polymerase II |
| RA | 62,471 | T→A | 5.2% | T330S (ACT→TCT) | polB ← | DNA polymerase II |
| RA | 62,472 | T→G | 5.2% | A329A (GCA→GCC) | polB ← | DNA polymerase II |
| RA | 62,484 | T→C | 5.3% | K325K (AAA→AAG) | polB ← | DNA polymerase II |
| RA | 72,621 | A→G | 7.1% | intergenic (+33/‑147) | ilvH → / → fruR | acetolactate synthase III, thiamin‑dependent, small subunit/DNA‑binding transcriptional dual regulator |
| RA | 72,624 | T→A | 7.2% | intergenic (+36/‑144) | ilvH → / → fruR | acetolactate synthase III, thiamin‑dependent, small subunit/DNA‑binding transcriptional dual regulator |
| RA | 72,627 | C→T | 7.4% | intergenic (+39/‑141) | ilvH → / → fruR | acetolactate synthase III, thiamin‑dependent, small subunit/DNA‑binding transcriptional dual regulator |
| RA | 129,042 | C→T | 9.4% | L201L (CTG→TTG) | yadH → | predicted transporter subunit |
| 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 | 56.9% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 214,931 | A→C | 57.1% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 225,827 | T→C | 8.2% | intergenic (+14/‑78) | gpt → / → frsA | guanine‑hypoxanthine phosphoribosyltransferase/hydrolase, binds to enzyme IIA(Glc) |
| RA | 266,222 | C→T | 6.7% | R128H (CGC→CAC) | yajO ← | predicted oxidoreductase, NAD(P)‑binding |
| RA | 1,028,431 | C→T | 8.7% | A462A (GCC→GCT) | malX → | fused maltose and glucose‑specific PTS enzyme IIBC components |
| RA | 1,036,505 | G→A | 100% | A632A (GCG→GCA) | rsxC → | fused predicted 4Fe‑4S ferredoxin‑type protein |
| RA | 1,262,097 | A→T | 7.8% | intergenic (‑49/+339) | torY ← / ← cutC | TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein |
| RA | 1,363,919 | G→T | 5.4% | R470L (CGC→CTC) | metG → | methionyl‑tRNA synthetase |
| RA | 1,364,064 | A→G | 5.9% | Q518Q (CAA→CAG) | metG → | methionyl‑tRNA synthetase |
| RA | 1,364,066 | C→G | 5.9% | P519R (CCG→CGG) | metG → | methionyl‑tRNA synthetase |
| RA | 1,364,068 | C→T | 7.2% | L520L (CTG→TTG) | metG → | methionyl‑tRNA synthetase |
| RA | 1,421,797 | C→T | 7.4% | T220T (ACG→ACA) | ccmF ← | heme lyase, CcmF subunit |
| RA | 1,746,320 | G→A | 5.7% | E247K (GAA→AAA) | srmB → | ATP‑dependent RNA helicase |
| RA | 1,763,556 | T→C | 44.3% | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,558 | G→C | 6.9% | noncoding (286/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,636 | A→G | 17.3% | noncoding (208/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,804,090 | G→A | 49.3% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 1,814,931 | A→G | 7.2% | G82G (GGT→GGC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 1,814,958 | A→G | 5.1% | G73G (GGT→GGC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 1,814,961 | A→G | 5.1% | G72G (GGT→GGC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 1,814,964 | C→G | 5.1% | A71A (GCG→GCC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 1,814,967 | A→G | 5.0% | R70R (CGT→CGC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 1,892,019:1 | +GC | 100% | intergenic (‑437/+54) | gudP ← / ← ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| RA | 2,064,071 | A→G | 6.1% | E104E (GAA→GAG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,064,080 | C→G | 6.5% | T107T (ACC→ACG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,064,086 | A→G | 5.2% | E109E (GAA→GAG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,064,095 | C→G | 5.3% | T112T (ACC→ACG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,065,001 | A→G | 5.5% | K414K (AAA→AAG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,065,007 | T→G | 5.7% | V416V (GTT→GTG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,065,010 | T→C | 5.4% | D417D (GAT→GAC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,065,013 | A→G | 6.0% | K418K (AAA→AAG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 2,068,683 | G→C | 7.8% | A369A (GCC→GCG) | aer ← | fused signal transducer for aerotaxis sensory component and methyl accepting chemotaxis component |
| RA | 2,068,689 | A→G | 6.5% | I367I (ATT→ATC) | aer ← | fused signal transducer for aerotaxis sensory component and methyl accepting chemotaxis component |
| RA | 2,086,490 | C→A | 5.8% | P89T (CCG→ACG) | yqjG → | predicted S‑transferase |
| RA | 2,139,798 | T→C | 11.1% | N437S (AAC→AGC) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,139,800 | T→C | 11.1% | E436E (GAA→GAG) ‡ | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,139,801 | T→G | 11.1% | E436A (GAA→GCA) ‡ | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,139,802 | C→G | 10.4% | E436Q (GAA→CAA) ‡ | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,139,803 | A→G | 10.5% | T435T (ACT→ACC) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,139,806 | T→G | 11.1% | E434D (GAA→GAC) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,139,809 | A→C | 10.3% | V433V (GTT→GTG) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,139,824 | A→G | 14.4% | I428I (ATT→ATC) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 2,257,303 | T→C | 6.7% | A1280A (GCA→GCG) | rpoB ← | RNA polymerase, beta subunit |
| RA | 2,266,165 | G→A | 7.8% | I93I (ATC→ATT) | tufB ← | protein chain elongation factor EF‑Tu |
| RA | 2,266,174 | T→C | 9.4% | K90K (AAA→AAG) | tufB ← | protein chain elongation factor EF‑Tu |
| RA | 2,266,177 | A→G | 9.6% | V89V (GTT→GTC) ‡ | tufB ← | protein chain elongation factor EF‑Tu |
| RA | 2,266,179 | C→T | 9.6% | V89I (GTT→ATT) ‡ | tufB ← | protein chain elongation factor EF‑Tu |
| RA | 2,266,180 | A→G | 9.6% | Y88Y (TAT→TAC) | tufB ← | protein chain elongation factor EF‑Tu |
| RA | 2,359,867 | G→A | 52.9% | noncoding (1228/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,876 | C→T | 51.0% | noncoding (1219/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,398,822 | T→G | 6.0% | V603V (GTA→GTC) | uvrD ← | DNA‑dependent ATPase I and helicase II |
| RA | 2,398,828 | A→G | 5.2% | V601V (GTT→GTC) | uvrD ← | DNA‑dependent ATPase I and helicase II |
| RA | 2,432,727 | A→G | 5.2% | I42I (ATT→ATC) | trxA ← | thioredoxin 1 |
| RA | 2,432,736 | G→A | 5.3% | I39I (ATC→ATT) | trxA ← | thioredoxin 1 |
| RA | 2,432,742 | T→C | 5.5% | K37K (AAA→AAG) | trxA ← | thioredoxin 1 |
| RA | 2,469,756 | T→C | 5.1% | Y246Y (TAT→TAC) | atpD → | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 2,494,963 | C→T | 7.4% | intergenic (+17/‑125) | ibpB → / → yidF | heat shock chaperone/predicted DNA‑binding transcriptional regulator |
| RA | 2,638,449 | C→T | 8.4% | R147R (CGC→CGT) | ugpC → | glycerol‑3‑phosphate transporter subunit |
| RA | 2,638,461 | C→T | 6.8% | R151R (CGC→CGT) | ugpC → | glycerol‑3‑phosphate transporter subunit |
| RA | 2,736,245 | A→G | 5.4% | E463E (GAA→GAG) | fusA → | protein chain elongation factor EF‑G |
| RA | 2,736,254 | C→G | 5.1% | L466L (CTC→CTG) | fusA → | protein chain elongation factor EF‑G |
| RA | 2,736,257 | C→A | 5.3% | D467E (GAC→GAA) | fusA → | protein chain elongation factor EF‑G |
| RA | 2,736,260 | C→T | 5.5% | I468I (ATC→ATT) | fusA → | protein chain elongation factor EF‑G |
| RA | 2,736,272 | T→C | 5.0% | R472R (CGT→CGC) | fusA → | protein chain elongation factor EF‑G |
| RA | 2,770,171 | G→A | 7.8% | V232M (GTG→ATG) | metA → | homoserine transsuccinylase |
| RA | 2,802,251 | A→G | 11.0% | S285S (TCT→TCC) | qor ← | quinone oxidoreductase, NADPH‑dependent |
| RA | 2,810,841 | A→C | 15.2% | F635L (TTT→TTG) ‡ | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,810,843 | A→T | 15.2% | F635I (TTT→ATT) ‡ | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,810,847 | A→G | 16.2% | G633G (GGT→GGC) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,810,858 | G→A | 15.9% | L630L (CTG→TTG) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,810,859 | C→G | 15.9% | T629T (ACG→ACC) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,810,865 | C→G | 15.9% | T627T (ACG→ACC) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,810,871 | G→A | 11.1% | D625D (GAC→GAT) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 2,827,243 | G→C | 8.4% | T336S (ACT→AGT) | dcuA ← | C4‑dicarboxylate antiporter |
| RA | 2,937,896 | C→T | 5.1% | intergenic (+23/‑246) | leuX → / → yjhV | tRNA‑Leu/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | Exported | = 7063 | 105 (0.990) | 26 (0.270) +GATT |
7/90 | NT | 32.7% | coding (897/1431 nt) | yaaJ | predicted transporter |
| ? | Exported | = 1611756 | 12 (0.110) | coding (1397/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | Exported | 62035 = | 66 (0.620) | 8 (0.080) | 3/90 | NT | 9.9% | coding (1424/2352 nt) | polB | DNA polymerase II |
| ? | Exported | 62063 = | 85 (0.870) | coding (1396/2352 nt) | polB | DNA polymerase II | |||||
| * | ? | Exported | 89211 = | 195 (1.840) | 13 (0.140) | 3/84 | NT | 8.1% | coding (490/1263 nt) | ftsA | ATP‑binding cell division protein involved in recruitment of FtsK to Z ring |
| ? | Exported | 89257 = | 129 (1.420) | coding (536/1263 nt) | ftsA | ATP‑binding cell division protein involved in recruitment of FtsK to Z ring | |||||
| * | ? | Exported | = 203035 | NA (NA) | 5 (0.050) | 3/92 | NT | NA | noncoding (440/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | Exported | = 203088 | NA (NA) | noncoding (493/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | Exported | = 203909 | NA (NA) | 5 (0.060) | 3/84 | NT | NA | noncoding (1314/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | Exported | = 203917 | NA (NA) | noncoding (1322/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | Exported | = 204740 | NA (NA) | 17 (0.190) | 5/82 | NT | NA | noncoding (157/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | Exported | = 204751 | NA (NA) | noncoding (168/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | Exported | = 206767 | NA (NA) | 15 (0.150) | 4/94 | NT | NA | noncoding (2184/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | Exported | = 206784 | NA (NA) | noncoding (2201/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | Exported | = 215622 | 48 (0.450) | 58 (1.250) +27 bp |
23/44 | NT | 68.7% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | Exported | 2705182 = | 73 (0.690) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | Exported | = 328743 | 124 (1.170) | 6 (0.060) | 3/90 | NT | 6.2% | coding (150/1305 nt) | gsk | inosine/guanosine kinase |
| ? | Exported | = 328786 | 67 (0.690) | coding (193/1305 nt) | gsk | inosine/guanosine kinase | |||||
| * | ? | Exported | = 344913 | 107 (1.010) | 14 (0.160) | 3/82 | NT | 11.4% | coding (526/678 nt) | ybbL | predicted transporter subunit |
| ? | Exported | = 344930 | 128 (1.450) | coding (543/678 nt) | ybbL | predicted transporter subunit | |||||
| * | ? | Exported | 436259 = | 83 (0.780) | 76 (0.780) | 35/90 | NT | 57.1% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | Exported | = 2706018 | 38 (0.390) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | Exported | = 436833 | 114 (1.070) | 150 (1.410) | 39/98 | NT | 57.1% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | Exported | 1803907 = | 111 (1.040) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | Exported | 566067 = | 141 (1.330) | 12 (0.130) | 3/86 | NT | 10.2% | coding (1682/1719 nt) | poxB | pyruvate dehydrogenase (pyruvate oxidase), thiamin‑dependent, FAD‑binding |
| ? | Exported | 566089 = | 87 (0.940) | coding (1660/1719 nt) | poxB | pyruvate dehydrogenase (pyruvate oxidase), thiamin‑dependent, FAD‑binding | |||||
| * | ? | Exported | = 1152546 | 79 (0.740) | 11 (0.120) | 3/82 | NT | 10.4% | coding (83/576 nt) | ydjR | conserved hypothetical protein |
| ? | Exported | = 1152570 | 123 (1.390) | coding (59/576 nt) | ydjR | conserved hypothetical protein | |||||
| * | ? | Exported | 1669623 = | 61 (0.570) | 8 (0.090) | 3/86 | NT | 13.7% | coding (420/1473 nt) | der | predicted GTP‑binding protein |
| ? | Exported | 1669653 = | 47 (0.510) | coding (390/1473 nt) | der | predicted GTP‑binding protein | |||||
| * | ? | Exported | 1994733 = | 75 (0.710) | 9 (0.090) | 3/88 | NT | 12.6% | coding (1417/2136 nt) | speC | ornithine decarboxylase, constitutive |
| ? | Exported | 1994757 = | 58 (0.610) | coding (1393/2136 nt) | speC | ornithine decarboxylase, constitutive | |||||
| * | ? | Exported | 2159817 = | 34 (0.320) | 6 (0.070) | 3/84 | NT | 10.2% | intergenic (+43/‑185) | ispB/sfsB | octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator |
| ? | Exported | 2159914 = | 77 (0.850) | intergenic (+140/‑88) | ispB/sfsB | octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator | |||||
| * | ? | Exported | 2356934 = | 119 (1.120) | 8 (0.080) | 3/88 | NT | 7.4% | coding (321/585 nt) | mobA | molybdopterin‑guanine dinucleotide synthase |
| ? | Exported | 2356958 = | 93 (0.980) | coding (345/585 nt) | mobA | molybdopterin‑guanine dinucleotide synthase | |||||
| * | ? | Exported | 2816800 = | 72 (0.680) | 4 (0.040) | 3/86 | NT | 6.0% | intergenic (+17/‑80) | soxR/nrfA | DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing/nitrite reductase, formate‑dependent, cytochrome |
| ? | Exported | 2816824 = | 62 (0.670) | intergenic (+41/‑56) | soxR/nrfA | DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing/nitrite reductase, formate‑dependent, cytochrome | |||||
| * | ? | Exported | = 2928756 | 138 (1.300) | 11 (0.120) | 3/88 | NT | 7.4% | coding (55/1083 nt) | yjgQ | conserved inner membrane protein |
| ? | Exported | = 2928777 | 150 (1.580) | coding (76/1083 nt) | yjgQ | conserved inner membrane protein | |||||