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 205 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | 1 | 90,424 | 0 | C | A | 77.0% | 303.6 / 100.5 | 178 | A13D (GCC→GAC) | unknown | hypothetical protein |
| * | 1 | 693,777 | 0 | A | . | 73.3% | 21.4 / 11.2 | 15 | coding (26/921 nt) | unknown | Glycosyl transferase, family 2 |
| * | 1 | 693,778 | 0 | T | . | 73.3% | 21.2 / 11.4 | 15 | coding (25/921 nt) | unknown | Glycosyl transferase, family 2 |
| * | 1 | 693,779 | 0 | T | . | 73.3% | 21.2 / 11.4 | 15 | coding (24/921 nt) | unknown | Glycosyl transferase, family 2 |
| * | 1 | 693,780 | 0 | G | . | 73.3% | 21.5 / 12.9 | 15 | coding (23/921 nt) | unknown | Glycosyl transferase, family 2 |
| * | 1 | 1,333,399 | 0 | A | . | 61.2% | 25.5 / 137.3 | 85 | intergenic (+39/‑14) | unknown/unknown | tRNA‑Leu‑TAA/tRNA‑Lys‑TTT |
| * | 1 | 1,333,400 | 0 | G | . | 60.5% | 13.5 / 155.7 | 86 | intergenic (+40/‑13) | unknown/unknown | tRNA‑Leu‑TAA/tRNA‑Lys‑TTT |
| * | 1 | 1,333,627 | 0 | C | A | 60.0% | 32.4 / 54.0 | 50 | S22Y (TCT→TAT) | unknown | Chromosome partitioning ATPase in PFGI‑1‑like cluster, ParA‑like |
| * | 1 | 1,063,970 | 0 | A | C | 57.4% | 19.4 / 55.6 | 54 | T1108P (ACC→CCC) | unknown | Chromosome partition protein MukB |
| * | 1 | 225,206 | 0 | A | . | 54.5% | 7.1 / 16.9 | 11 | coding (119/375 nt) | unknown | hypothetical protein |
| * | 1 | 225,207 | 0 | G | . | 54.5% | 7.6 / 19.6 | 11 | coding (118/375 nt) | unknown | hypothetical protein |
| * | 1 | 1,333,488 | 1 | . | A | 50.0% | 48.9 / 230.9 | 106 | noncoding (76/76 nt) | unknown | tRNA‑Lys‑TTT |
| * | 1 | 1,333,488 | 2 | . | G | 50.0% | 57.0 / 251.2 | 106 | noncoding (76/76 nt) | unknown | tRNA‑Lys‑TTT |
| * | 1 | 630,474 | 0 | T | G | 49.2% | 56.4 / 24.9 | 66 | L54V (TTG→GTG) | unknown | N‑acetylmannosamine‑6‑phosphate 2‑epimerase (EC 5.1.3.9) |
| * | 1 | 1,333,553 | 0 | T | C | 48.4% | 7.4 / 96.5 | 93 | intergenic (+65/‑10) | unknown/unknown | tRNA‑Lys‑TTT/Chromosome partitioning ATPase in PFGI‑1‑like cluster, ParA‑like |
| * | 1 | 1,333,518 | 0 | A | G | 47.6% | 20.0 / 107.2 | 103 | intergenic (+30/‑45) | unknown/unknown | tRNA‑Lys‑TTT/Chromosome partitioning ATPase in PFGI‑1‑like cluster, ParA‑like |
| * | 1 | 1,333,566 | 0 | T | A | 47.1% | 51.2 / 124.5 | 87 | C2S (TGC→AGC) | unknown | Chromosome partitioning ATPase in PFGI‑1‑like cluster, ParA‑like |
| * | 1 | 1,333,569 | 0 | A | G | 47.1% | 17.4 / 86.9 | 87 | I3V (ATT→GTT) | unknown | Chromosome partitioning ATPase in PFGI‑1‑like cluster, ParA‑like |
| * | 1 | 1,333,500 | 0 | C | T | 47.1% | 28.5 / 96.3 | 102 | intergenic (+12/‑63) | unknown/unknown | tRNA‑Lys‑TTT/Chromosome partitioning ATPase in PFGI‑1‑like cluster, ParA‑like |
| * | 1 | 1,333,502 | 1 | . | A | 47.1% | 70.5 / 206.6 | 102 | intergenic (+14/‑61) | unknown/unknown | tRNA‑Lys‑TTT/Chromosome partitioning ATPase in PFGI‑1‑like cluster, ParA‑like |
| Marginal new junction evidence (lowest skew 10 of 72 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | 12 | = 486 | 0 (0.000) | 9 (0.080) | 4/430 | 3.2 | 100% | coding (486/486 nt) | unknown | 3'(2'),5'‑bisphosphate nucleotidase (EC 3.1.3.7) |
| ? | 4 | 1 = | 0 (0.000) | coding (135/135 nt) | unknown | 3'(2'),5'‑bisphosphate nucleotidase (EC 3.1.3.7) | |||||
| * | ? | 1 | 1009324 = | 4 (0.050) | 22 (0.300) | 15/376 | 3.2 | 92.6% | intergenic (+172/‑89) | unknown/unknown | Threonyl‑tRNA synthetase (EC 6.1.1.3)/Type III restriction‑modification system methylation subunit (EC 2.1.1.72) |
| ? | 1 | = 1009313 | 0 (0.000) | intergenic (+161/‑100) | unknown/unknown | Threonyl‑tRNA synthetase (EC 6.1.1.3)/Type III restriction‑modification system methylation subunit (EC 2.1.1.72) | |||||
| * | ? | 1 | 693781 = | 2 (0.020) | 15 (0.200) | 14/392 | 3.6 | 94.3% | coding (22/921 nt) | unknown | Glycosyl transferase, family 2 |
| ? | 1 | = 693776 | 0 (0.000) | coding (27/921 nt) | unknown | Glycosyl transferase, family 2 | |||||
| * | ? | 1 | 669993 = | 77 (0.920) | 6 (0.100) +86 bp |
6/258 | 4.2 | 20.7% | intergenic (+26/‑156) | unknown/unknown | tRNA‑Pro‑TGG/SSU rRNA ## 16S rRNA, small subunit ribosomal RNA |
| ? | 2 | = 176511 | 0 (0.000) | intergenic (‑277/–) | unknown/– | Transaldolase (EC 2.2.1.2)/– | |||||
| * | ? | 1 | = 1310348 | 92 (1.090) | 8 (0.140) +76 bp |
6/278 | 4.5 | 13.8% | coding (213/645 nt) | unknown | Putative transposase InsK for insertion sequence element IS150 |
| ? | 3 | 20593 = | 63 (0.650) | coding (181/348 nt) | unknown | hypothetical protein | |||||
| * | ? | 1 | 673420 = | NA (NA) | 12 (0.150) | 9/396 | 5.0 | NA | noncoding (1165/3023 nt) | unknown | LSU rRNA ## 23S rRNA, large subunit ribosomal RNA |
| ? | 1 | 673559 = | NA (NA) | noncoding (1304/3023 nt) | unknown | LSU rRNA ## 23S rRNA, large subunit ribosomal RNA | |||||
| * | ? | 1 | 623657 = | 65 (0.770) | 14 (0.170) +G |
10/428 | 5.0 | 30.2% | intergenic (+144/+532) | unknown/unknown | Outer membrane protein A precursor/PTS system, N‑acetylglucosamine‑specific IIC component / PTS system, N‑acetylglucosamine‑specific IIB component (EC 2.7.1.193) |
| ? | 1 | 1202140 = | 0 (0.000) | intergenic (+131/+464) | unknown/unknown | Na+/H+ antiporter/LSU rRNA ## 23S rRNA, large subunit ribosomal RNA | |||||
| * | ? | 1 | 1299093 = | NA (NA) | 19 (0.270) +36 bp |
7/358 | 5.2 | 57.3% | intergenic (‑177/+395) | unknown/unknown | tRNA‑Asp‑GTC/LSU rRNA ## 23S rRNA, large subunit ribosomal RNA |
| ? | 1 | = 1657605 | 17 (0.200) | intergenic (‑147/+94) | unknown/unknown | Transposase, IS200 family/CTP synthase (EC 6.3.4.2) | |||||
| * | ? | 2 | = 154908 | 96 (0.900) | 23 (0.230) +ATTT |
11/412 | 6.3 | 31.0% | intergenic (‑271/+796) | unknown/unknown | Deoxyribose‑phosphate aldolase (EC 4.1.2.4)/hypothetical protein |
| ? | 3 | = 20679 | 6 (0.060) | coding (95/348 nt) | unknown | hypothetical protein | |||||
| * | ? | 1 | 1202140 = | 2 (0.020) | 9 (0.110) +C |
6/428 | 6.4 | 24.4% | intergenic (+131/+464) | unknown/unknown | Na+/H+ antiporter/LSU rRNA ## 23S rRNA, large subunit ribosomal RNA |
| ? | 1 | = 1648073 | 54 (0.640) | intergenic (+40/+88) | unknown/unknown | hypothetical protein/LSU ribosomal protein L17p | |||||