| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | BS168_reference_genome | 2,581,726:1 | +T | 100% | intergenic (‑109/+45) | pstS ← / ← pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | BS168_reference_genome | 2,581,726 | 1 | . | T | 95.5% | 143.7 / 0.1 | 44 | intergenic (‑109/+45) | pstS/pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base T (34/8); total (34/10) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.76e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
ATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑G‑TTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCT > BS168_reference_genome/2581602‑2581850 | aTTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑aa > 2:51865/1‑138 (MQ=255) tttCATTTAGTTAATCCCCCCTGCTTAAAATTTGAATTTTGCCCTACCCTTAAAGAGTAAAGGTTATATGTAA‑AACGGGTTTCAACCGAATGTTAAGGTTTTGTAAATCAGTGG‑GTTTTTTTGA‑AA‑AAAAAAAACGcc < 2:26716/138‑1 (MQ=255) tgtAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATTAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTAt > 3:180590/1‑136 (MQ=255) tgtAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTAt > 5:78133/1‑136 (MQ=255) gtAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCag > 5:89587/1‑138 (MQ=255) gtAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATAag > 2:208105/1‑138 (MQ=255) tAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑ATAAAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCag > 4:192565/1‑138 (MQ=255) tAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCag > 6:119288/1‑137 (MQ=255) tAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCACACATCATGTCAGCGTTTTATTTTAGTTATCaga > 4:201466/1‑138 (MQ=255) ccTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTtgt > 3:73480/1‑139 (MQ=255) ccTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTtgt > 5:294583/1‑139 (MQ=255) cacGTATAGATTAAAGGTTATA‑GTAACAACGGGTTTGACCCGAATTTTACGGTTTTGTAAATCAGTGCTT‑TTTTTTTT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGttt < 8:246264/139‑1 (MQ=255) ataGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTg > 7:183905/1‑138 (MQ=255) tAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttc > 5:256087/1‑139 (MQ=255) tAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTATTTTTTTAGTTATCAGAAGACGTAGTGTTTTCTGCATTttc > 2:38767/1‑139 (MQ=255) aaGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTTT‑AT‑AAAAAAAACGCCCCCATCATGTGAGCGTTTTTTTTTAGTTTTCTGAAGACGTGGTGTTTTATGAATTttct > 7:157760/1‑138 (MQ=255) aaGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑ATAAAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGATGACGTTGTGTTTTCTGCATTttct > 2:267002/1‑139 (MQ=255) aaGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt > 5:121372/1‑139 (MQ=255) aaGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt < 6:126960/139‑1 (MQ=255) aaGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttct > 1:16546/1‑138 (MQ=255) aGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt > 6:122405/1‑138 (MQ=255) caaTGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTAGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAATTAACAGAAGACGTTGTGTTTAATGCATTTTCTAAAAttt > 2:116715/3‑139 (MQ=255) cTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 6:218898/1‑139 (MQ=255) cTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 6:22006/1‑139 (MQ=255) cTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 7:153634/1‑139 (MQ=255) cTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 1:77746/1‑139 (MQ=255) cTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTAAGTTTTCAGAAGAAGTTGTGTTTTCTGCATTATCTTCAAttt > 1:57514/1‑139 (MQ=255) cTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGATTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACTCCCACATCATGTGATCGTGTTTTTTTAGTTATCAGAATAAGTTGTGTTTTCTGCATATTCTT‑AAtttt > 4:268412/1‑139 (MQ=255) cTATGTAA‑AAAGGGTTTGAAACGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACCCCCACATCATGTGAGCGTGTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 8:13222/1‑139 (MQ=255) tattaaa‑aaaGGGTTTTAACCGATTGTTACGGTTTTGTAAATCAGTGC‑GTTTTTTTTT‑AA‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt < 2:16546/133‑1 (MQ=255) aTGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTg > 4:207466/1‑139 (MQ=255) a‑aaaGGGTTTGAACCGAATGTTAAGGTTTTTAAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCtt < 6:51617/138‑1 (MQ=255) a‑aaaGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCttt > 6:83270/1‑139 (MQ=255) aaaGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTa > 5:168168/1‑139 (MQ=255) gttctaaCCGAATTTTAAGGTTTTTTAAAACTGTGC‑G‑TTTTTTTTAAA‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCtt < 6:89587/134‑1 (MQ=255) aTGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 5:119288/139‑1 (MQ=255) aTGTTAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 8:153634/139‑1 (MQ=255) aTGTTAAGGTTTTGAAAATCAGTGC‑GTTTTTTTGA‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 7:151236/139‑1 (MQ=255) tAAGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACcttc > 7:107400/1‑139 (MQ=255) aGGTTTTGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGAATTTTCTTCAATTTTGTCTTTATTCTTTTTCTGAGTACcttctt > 4:266529/1‑139 (MQ=255) tGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCTGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCt > 7:61663/1‑139 (MQ=255) tGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGt > 8:7148/1‑136 (MQ=255) tGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGt < 7:7148/136‑1 (MQ=255) tGTAAATCAGTGC‑GTTTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTccc > 5:161719/1‑138 (MQ=255) | ATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAA‑AAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGC‑G‑TTTTTTGT‑AT‑AAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCT > BS168_reference_genome/2581602‑2581850 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |