mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 118 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | 1 | 1,147,516 | 0 | C | T | 54.5% | 19.3 / 48.5 | 33 | V139V (GTG→GTA) | unknown | ABC‑type Fe3+ transport system, periplasmic component |
| * | 1 | 1,147,522 | 0 | G | A | 53.1% | 20.3 / 46.4 | 32 | R137R (CGC→CGT) | unknown | ABC‑type Fe3+ transport system, periplasmic component |
| * | 1 | 1,275,683 | 0 | T | G | 50.0% | 42.2 / 15.4 | 36 | T1108P (ACC→CCC) | unknown | Chromosome partition protein MukB |
| * | 1 | 2,095,224 | 0 | A | C | 50.0% | 103.8 / 17.2 | 68 | N311T (AAC→ACC) | unknown | 23S rRNA (uracil(747)‑C(5))‑methyltransferase (EC 2.1.1.189) |
| * | 1 | 1,147,527 | 0 | T | G | 48.4% | 38.5 / 13.6 | 31 | T136P (ACC→CCC) | unknown | ABC‑type Fe3+ transport system, periplasmic component |
| * | 1 | 1,910,121 | 0 | T | G | 44.6% | 124.3 / 11.8 | 65 | D381A (GAC→GCC) | unknown | Replication‑associated recombination protein RarA |
| * | 1 | 1,233,866 | 0 | T | G | 44.0% | 150.7 / 17.8 | 91 | V324G (GTG→GGG) | unknown | Phenylalanyl‑tRNA synthetase beta chain (EC 6.1.1.20) |
| * | 1 | 246,776 | 0 | A | C | 42.1% | 91.0 / 17.0 | 58 | H30P (CAC→CCC) | unknown | tRNA‑dihydrouridine(20/20a) synthase (EC 1.3.1.91) |
| * | 1 | 1,910,059 | 0 | C | T | 41.5% | 61.2 / 22.7 | 54 | E402K (GAA→AAA) | unknown | Replication‑associated recombination protein RarA |
| * | 1 | 154,204 | 0 | G | T | 41.4% | 116.8 / 21.1 | 60 | C609F (TGC→TTC) | unknown | Ribonucleotide reductase of class III (anaerobic), large subunit (EC 1.17.4.2) |
| * | 1 | 1,866,526 | 0 | T | G | 40.5% | 66.4 / 12.0 | 42 | T614P (ACC→CCC) | unknown | [NiFe] hydrogenase metallocenter assembly protein HypF |
| * | 1 | 1,985,101 | 0 | T | G | 40.3% | 113.9 / 14.1 | 63 | T275P (ACC→CCC) | unknown | 16S rRNA (guanine(1207)‑N(2))‑methyltransferase (EC 2.1.1.172) |
| * | 1 | 1,226,987 | 0 | A | C | 40.3% | 103.8 / 13.9 | 72 | V449G (GTG→GGG) | unknown | Anthranilate synthase, aminase component (EC 4.1.3.27) |
| * | 1 | 1,482,294 | 0 | T | G | 39.4% | 137.9 / 16.1 | 66 | Y879S (TAC→TCC) | unknown | hypothetical protein |
| * | 1 | 1,709,179 | 0 | A | C | 39.1% | 89.6 / 12.7 | 46 | L54V (TTG→GTG) | unknown | N‑acetylmannosamine‑6‑phosphate 2‑epimerase (EC 5.1.3.9) |
| * | 1 | 1,938,508 | 0 | T | G | 38.9% | 95.5 / 15.4 | 54 | V80G (GTG→GGG) | unknown | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase (EC 2.4.99.17) |
| * | 1 | 1,047,106 | 0 | G | A | 38.0% | 102.0 / 28.5 | 71 | S61F (TCC→TTC) | unknown | Sulfate transporter, CysZ‑type |
| * | 1 | 1,107,460 | 0 | G | A | 37.8% | 68.6 / 15.5 | 45 | N133N (AAC→AAT) | unknown | Long‑chain fatty acid transport protein |
| * | 1 | 1,938,523 | 0 | T | G | 37.7% | 104.9 / 11.3 | 53 | V85G (GTG→GGG) | unknown | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase (EC 2.4.99.17) |
| * | 1 | 1,073,761 | 0 | C | A | 36.7% | 94.2 / 12.5 | 49 | L191I (CTT→ATT) | unknown | 4‑hydroxy‑2‑oxoglutarate aldolase (EC 4.1.3.16) @ 2‑dehydro‑3‑deoxyphosphogluconate aldolase (EC 4.1.2.14) |
| Marginal new junction evidence (lowest skew 10 of 137 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | 1 | = 642882 | 90 (1.330) | 19 (0.290) | 9/444 | 3.8 | 18.6% | coding (135/810 nt) | unknown | 3'(2'),5'‑bisphosphate nucleotidase (EC 3.1.3.7) |
| ? | 1 | = 643368 | 78 (1.180) | coding (621/810 nt) | unknown | 3'(2'),5'‑bisphosphate nucleotidase (EC 3.1.3.7) | |||||
| * | ? | 1 | 263951 = | NA (NA) | 16 (0.260) | 8/420 | 3.9 | NA | noncoding (1303/3023 nt) | unknown | LSU rRNA ## 23S rRNA, large subunit ribosomal RNA |
| ? | 1 | 264090 = | NA (NA) | noncoding (1164/3023 nt) | unknown | LSU rRNA ## 23S rRNA, large subunit ribosomal RNA | |||||
| * | ? | 1 | 508965 = | 110 (1.630) | 18 (0.280) | 8/432 | 4.0 | 15.8% | coding (349/861 nt) | unknown | Acetolactate synthase large subunit (EC 2.2.1.6) |
| ? | 1 | 509810 = | 87 (1.350) | coding (260/408 nt) | unknown | Threonine dehydratase biosynthetic (EC 4.3.1.19) | |||||
| * | ? | 1 | 1449278 = | 58 (0.860) | 18 (0.270) | 7/444 | 4.3 | 21.9% | coding (1333/1494 nt) | unknown | PTS system, N‑acetylmannosamine‑specific IIC component / PTS system, N‑acetylmannosamine‑specific IIB component |
| ? | 1 | 1449405 = | 72 (1.090) | coding (1206/1494 nt) | unknown | PTS system, N‑acetylmannosamine‑specific IIC component / PTS system, N‑acetylmannosamine‑specific IIB component | |||||
| * | ? | 1 | = 926371 | 52 (0.770) | 8 (0.130) | 6/426 | 4.5 | 13.8% | intergenic (‑166/+361) | unknown/unknown | Soluble lytic murein transglycosylase (EC 4.2.2.n1)/YciL protein |
| ? | 1 | = 926650 | 51 (0.810) | intergenic (‑445/+82) | unknown/unknown | Soluble lytic murein transglycosylase (EC 4.2.2.n1)/YciL protein | |||||
| * | ? | 1 | = 1818536 | 57 (0.840) | 8 (0.120) | 6/442 | 4.6 | 11.6% | coding (411/1734 nt) | unknown | Efflux ABC transporter for glutathione/L‑cysteine, essential for assembly of bd‑type respiratory oxidases => CydC subunit |
| ? | 1 | = 1818720 | 66 (1.000) | coding (595/1734 nt) | unknown | Efflux ABC transporter for glutathione/L‑cysteine, essential for assembly of bd‑type respiratory oxidases => CydC subunit | |||||
| * | ? | 1 | = 641697 | 86 (1.270) | 7 (0.110) | 6/434 | 4.6 | 8.6% | coding (1484/2007 nt) | unknown | Predicted membrane protein |
| ? | 1 | = 641902 | 66 (1.020) | coding (1689/2007 nt) | unknown | Predicted membrane protein | |||||
| * | ? | 1 | = 595447 | 71 (1.050) | 12 (0.190) | 6/436 | 4.6 | 15.7% | coding (142/312 nt) | unknown | Zn‑ribbon‑containing, possibly RNA‑binding protein and truncated derivatives |
| ? | 1 | = 595583 | 61 (0.940) | coding (6/312 nt) | unknown | Zn‑ribbon‑containing, possibly RNA‑binding protein and truncated derivatives | |||||
| * | ? | 1 | 510484 = | 90 (1.330) | 7 (0.110) | 6/430 | 4.6 | 6.8% | intergenic (+59/+75) | unknown/unknown | Threonine dehydratase biosynthetic (EC 4.3.1.19)/Cell‑division‑associated, ABC‑transporter‑like signaling protein FtsX |
| ? | 1 | 510711 = | 106 (1.660) | coding (784/936 nt) | unknown | Cell‑division‑associated, ABC‑transporter‑like signaling protein FtsX | |||||
| * | ? | 1 | 5369 = | NA (NA) | 9 (0.140) | 6/440 | 4.6 | NA | coding (184/375 nt) | unknown | hypothetical protein |
| ? | 1 | 5947 = | NA (NA) | coding (346/762 nt) | unknown | Mobile element protein | |||||