mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 29,154 | G→C | 7.7% | V220V (GTG→GTC) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 29,157 | G→T | 7.6% | V221V (GTG→GTT) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 29,160 | T→C | 6.7% | R222R (CGT→CGC) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 29,163 | T→C | 6.7% | D223D (GAT→GAC) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 29,166 | A→G | 7.3% | K224K (AAA→AAG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 36,434 | G→A | 13.9% | I120I (ATC→ATT) | caiB ← | crotonobetainyl CoA:carnitine CoA transferase |
| 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 | 45.1% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 214,931 | A→C | 44.0% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 282,462 | C→T | 17.9% | A59T (GCA→ACA) | yajG ← | predicted lipoprotein |
| RA | 324,001 | C→T | 12.3% | T138I (ACC→ATC) | htpG → | molecular chaperone HSP90 family |
| RA | 483,085 | G→T | 11.5% | A97S (GCG→TCG) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 494,477 | C→T | 17.0% | L272L (CTG→CTA) | galM ← | galactose‑1‑epimerase |
| RA | 538,165 | C→T | 15.4% | S280L (TCG→TTG) | rhlE → | RNA helicase |
| RA | 573,576 | A→G | 20.7% | G135G (GGA→GGG) | ybjD → | conserved hypothetical protein with nucleoside triphosphate hydrolase domain |
| RA | 705,870 | A→G | 35.7% | intergenic (‑367/+128) | ymcC ← / ← serX | predicted outer membrane lipoprotein/tRNA‑Ser |
| RA | 826,990 | G→A | 14.9% | N173N (AAC→AAT) | narL ← | DNA‑binding response regulator in two‑component regulatory system with NarX (or NarQ) |
| RA | 857,256 | A→C | 10.9% | D38E (GAT→GAG) | trpB ← | tryptophan synthase, beta subunit |
| RA | 977,473 | C→T | 14.5% | D558N (GAT→AAT) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 992,906 | G→T | 9.5% | intergenic (+95/‑100) | dmsD → / → clcB | twin‑argninine leader‑binding protein for DmsA and TorA/predicted voltage‑gated chloride channel |
| RA | 1,005,656 | G→A | 8.1% | intergenic (‑62/‑462) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/hypothetical protein |
| RA | 1,015,742 | G→A | 12.1% | G109G (GGC→GGT) | fumA ← | aerobic Class I fumarate hydratase |
| RA | 1,020,547 | G→A | 17.7% | intergenic (‑5/+34) | uidC ← / ← uidB | predicted outer membrane porin protein/glucuronide transporter |
| RA | 1,036,505 | G→A | 100% | A632A (GCG→GCA) | rsxC → | fused predicted 4Fe‑4S ferredoxin‑type protein |
| RA | 1,047,174 | G→A | 24.1% | I40I (ATC→ATT) | ydhH ← | conserved hypothetical protein |
| RA | 1,049,684 | G→A | 12.9% | D244N (GAT→AAT) | ydhJ → | undecaprenyl pyrophosphate phosphatase |
| RA | 1,071,476 | G→A | 20.0% | G110D (GGT→GAT) | mdtK → | multidrug efflux system transporter |
| RA | 1,125,754 | C→T | 8.2% | A294T (GCC→ACC) | pheS ← | phenylalanine tRNA synthetase, alpha subunit |
| RA | 1,150,016 | G→A | 12.5% | intergenic (‑69/‑133) | osmE ← / → nadE | DNA‑binding transcriptional regulator/NAD synthetase, NH3/glutamine‑dependent |
| RA | 1,171,017 | T→A | 21.5% | L319Q (CTG→CAG) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,194,880 | C→T | 14.6% | A102T (GCG→ACG) | yeaZ ← | predicted peptidase |
| RA | 1,208,527 | G→A | 8.7% | M242I (ATG→ATA) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,212,559 | T→C | 8.7% | N42D (AAC→GAC) | yobG ← | hypothetical protein |
| RA | 1,216,248 | A→G | 9.2% | V82A (GTA→GCA) | htpX ← | predicted endopeptidase |
| RA | 1,224,379 | G→A | 13.7% | E81K (GAA→AAA) | yebU → | predicted methyltransferase |
| RA | 1,225,405 | G→A | 21.0% | E423K (GAG→AAG) | yebU → | predicted methyltransferase |
| RA | 1,316,293 | G→A | 22.1% | G58S (GGC→AGC) | hisF → | imidazole glycerol phosphate synthase, catalytic subunit with HisF |
| RA | 1,326,669 | C→T | 17.1% | L114L (CTG→CTA) | wcaK ← | predicted pyruvyl transferase |
| RA | 1,380,514 | T→C | 6.2% | I62V (ATT→GTT) | galS ← | DNA‑binding transcriptional repressor |
| RA | 1,394,860:1 | +G | 19.4% | coding (68/1131 nt) | fruB ← | fused fructose‑specific PTS enzyme IIA component and HPr component |
| RA | 1,417,802 | A→G | 6.0% | intergenic (+83/‑250) | proL → / → narP | tRNA‑Pro/DNA‑binding response regulator in two‑component regulatory system with NarQ or NarX |
| RA | 1,417,804 | C→T | 5.3% | intergenic (+85/‑248) | proL → / → narP | tRNA‑Pro/DNA‑binding response regulator in two‑component regulatory system with NarQ or NarX |
| RA | 1,751,234 | G→T | 14.1% | intergenic (‑20/‑187) | yfiF ← / → trxC | predicted methyltransferase/thioredoxin 2 |
| RA | 1,755,070 | C→T | 11.7% | A811V (GCT→GTT) | yfiQ → | fused predicted acyl‑CoA synthetase NAD(P)‑binding subunit and ATP‑binding subunit |
| RA | 1,763,556 | T→C | 36.2% | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,636 | A→G | 32.3% | noncoding (208/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,804,090 | G→A | 42.6% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 1,823,089 | A→G | 9.6% | L320L (TTA→TTG) | norW → | NADH:flavorubredoxin oxidoreductase |
| RA | 1,892,019:1 | +GC | 100% | intergenic (‑437/+54) | gudP ← / ← ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| RA | 1,970,940 | C→G | 8.0% | E656Q (GAA→CAA) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 1,970,946 | A→G | 5.4% | Y654H (TAT→CAT) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 2,033,597 | G→A | 8.0% | S12N (AGC→AAC) | tolC → | transport channel |
| RA | 2,235,971 | C→T | 13.0% | R373C (CGT→TGT) | purH → | fused IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 2,253,725 | C→T | 15.1% | A1105T (GCG→ACG) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,331,736 | C→T | 6.9% | S208N (AGC→AAC) | fdhD ← | formate dehydrogenase formation protein |
| RA | 2,344,483 | C→A | 23.5% | G383G (GGC→GGA) | glnG → | fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI) |
| RA | 2,359,192 | G→A | 9.4% | noncoding (1903/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,867 | G→A | 27.5% | noncoding (1228/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,876 | C→T | 22.7% | noncoding (1219/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,387,702 | G→A | 14.7% | L238L (CTG→TTG) | yigL ← | predicted hydrolase |
| RA | 2,417,803 | T→C | 14.4% | intergenic (‑77/+114) | yifK ← / ← rffM | predicted transporter/UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 2,418,274 | C→T | 13.1% | L128L (CTG→CTA) | rffM ← | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 2,648,029 | A→G | 6.7% | N146S (AAC→AGC) | glgB → | 1,4‑alpha‑glucan branching enzyme |
| RA | 2,795,595 | G→T | 17.5% | E29* (GAA→TAA) | dgkA → | diacylglycerol kinase |
| RA | 2,817,653 | A→G | 7.2% | P258P (CCA→CCG) | nrfA → | nitrite reductase, formate‑dependent, cytochrome |
| RA | 2,823,545 | C→T | 10.2% | intergenic (+290/+668) | nrfG → / ← pheU | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe |
| RA | 2,826,736 | G→A | 9.3% | P95S (CCT→TCT) | cutA ← | copper binding protein, copper sensitivity |
| RA | 2,861,362 | A→G | 22.2% | Q150R (CAG→CGG) | miaA → | delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase |
| RA | 2,882,226 | G→A | 15.4% | E24E (GAG→GAA) | ytfH → | predicted transcriptional regulator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | minE | 251990 | 252039 | 50 | 19 [17] | [16] 20 | malZ | maltodextrin glucosidase |
| * | * | ÷ | minE | 444386 | 444417 | 32 | 18 [16] | [15] 18 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | minE | 1616710 | 1616756 | 47 | 18 [17] | [17] 18 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | minE | = 7063 | 63 (0.910) | 33 (0.520) +GATT |
9/96 | NT | 50.6% | coding (897/1431 nt) | yaaJ | predicted transporter |
| ? | minE | = 1611756 | 7 (0.100) | coding (1397/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | minE | 18301 = | 81 (1.170) | 8 (0.120) | 4/102 | NT | 9.4% | intergenic (+140/+192) | nhaR/rpsT | DNA‑binding transcriptional activator/30S ribosomal subunit protein S20 |
| ? | minE | 18320 = | 74 (1.090) | intergenic (+159/+173) | nhaR/rpsT | DNA‑binding transcriptional activator/30S ribosomal subunit protein S20 | |||||
| * | ? | minE | = 170738 | 70 (1.010) | 5 (0.080) | 3/92 | NT | 7.8% | coding (59/726 nt) | pyrH | uridylate kinase |
| ? | minE | = 170755 | 56 (0.920) | coding (76/726 nt) | pyrH | uridylate kinase | |||||
| * | ? | minE | = 204740 | NA (NA) | 4 (0.070) | 3/88 | NT | NA | noncoding (157/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | minE | = 204751 | NA (NA) | noncoding (168/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | minE | = 215622 | 68 (0.990) | 23 (0.710) +27 bp |
17/50 | NT | 36.9% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | minE | 2705182 = | 99 (1.430) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | minE | 409805 = | 91 (1.320) | 4 (0.070) | 3/86 | NT | 5.6% | coding (2551/2583 nt) | leuS | leucyl‑tRNA synthetase |
| ? | minE | 409827 = | 59 (1.040) | coding (2529/2583 nt) | leuS | leucyl‑tRNA synthetase | |||||
| * | ? | minE | 436259 = | 48 (0.700) | 38 (0.600) | 21/96 | NT | 49.0% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | minE | = 2706018 | 35 (0.550) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | minE | = 436833 | 100 (1.450) | 62 (0.900) | 37/104 | NT | 40.4% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | minE | 1803907 = | 83 (1.200) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | minE | = 1015094 | 58 (0.840) | 8 (0.120) | 3/98 | NT | 13.6% | coding (975/1647 nt) | fumA | aerobic Class I fumarate hydratase |
| ? | minE | = 1015113 | 47 (0.720) | coding (956/1647 nt) | fumA | aerobic Class I fumarate hydratase | |||||
| * | ? | minE | 1066657 = | 81 (1.170) | 5 (0.080) | 3/94 | NT | 6.6% | coding (833/933 nt) | ydhB | predicted DNA‑binding transcriptional regulator |
| ? | minE | 1066681 = | 68 (1.090) | coding (809/933 nt) | ydhB | predicted DNA‑binding transcriptional regulator | |||||
| * | ? | minE | 1712410 = | 66 (0.960) | 5 (0.080) | 3/90 | NT | 8.9% | coding (3022/3282 nt) | yphG | conserved hypothetical protein |
| ? | minE | 1712433 = | 45 (0.760) | coding (2999/3282 nt) | yphG | conserved hypothetical protein | |||||
| * | ? | minE | = 1881475 | 51 (0.740) | 4 (0.060) | 3/94 | NT | 7.3% | coding (1659/2235 nt) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| ? | minE | = 1881494 | 56 (0.900) | coding (1640/2235 nt) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase | |||||
| * | ? | minE | 2726679 = | 46 (0.670) | 3 (0.050) | 3/92 | NT | 6.7% | coding (404/1914 nt) | yheS | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| ? | minE | 2726703 = | 43 (0.710) | coding (380/1914 nt) | yheS | fused predicted transporter subunits and ATP‑binding components of ABC superfamily | |||||