| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 481,301:1 | +TATCATC | 100% | coding (85/648 nt) | acrR → | transcriptional repressor |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 481,301 | 1 | . | T | 81.8% | 23.7 / 1.3 | 11 | coding (85/648 nt) | acrR | transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base T (5/4); total (5/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| * | CP009273 | 481,301 | 2 | . | A | 81.8% | 21.6 / 1.2 | 11 | coding (85/648 nt) | acrR | transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base A (5/4); total (5/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| * | CP009273 | 481,301 | 3 | . | T | 81.8% | 23.2 / 1.3 | 11 | coding (85/648 nt) | acrR | transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base T (5/4); total (5/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| * | CP009273 | 481,301 | 4 | . | C | 81.8% | 26.6 / 1.5 | 11 | coding (85/648 nt) | acrR | transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (5/4); total (5/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| * | CP009273 | 481,301 | 5 | . | A | 81.8% | 22.1 / 1.2 | 11 | coding (85/648 nt) | acrR | transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base A (5/4); total (5/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| * | CP009273 | 481,301 | 6 | . | T | 81.8% | 25.3 / 1.3 | 11 | coding (85/648 nt) | acrR | transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base T (5/4); total (5/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| * | CP009273 | 481,301 | 7 | . | C | 81.8% | 26.4 / 1.5 | 11 | coding (85/648 nt) | acrR | transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (5/4); total (5/6) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.55e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
AGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTCACAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGG‑‑‑‑‑‑‑TATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATCCACTCTC > CP009273/481029‑481476 ||||||| agCATCAGAACGACCGCCAGATGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTCACAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGG‑‑‑‑‑‑‑t < 1:48360/274‑1 (MQ=255) catacatTCACAAATGTATGTAAATCTGACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTAcgc > 1:200290/1‑190 (MQ=255) tacatTCACAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGCGCTTGCAAAAGCAGCTGGCGTTACGCGCGGTGCCATCTACTGGCATTTTAAAGAAAAGTCGGATTTGTTCAGTGGGATCGGGGAACTGTCAGAATCCAATATTGgagacgcac > 2:51672/1‑270 (MQ=255) catTCACAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCgg < 2:200284/190‑1 (MQ=255) atgtaAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCAAATATTGGTGAACTAGAGCTTGAGTATCAga > 1:179620/1‑274 (MQ=255) aCGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCAAAAATTGGTGAACTAGAGCTTGAGTATCACACCAAATGcccc > 2:17300/1‑274 (MQ=255) tAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATc < 1:51673/275‑1 (MQ=255) aaTTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGCTGTGGCTCTACGTCTTTTCTCACAGCAGGGGG‑‑‑‑‑‑‑Ta < 1:221352/100‑1 (MQ=255) aCGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATCCACtctc < 1:17300/275‑1 (MQ=255) ggCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCAttt > 1:94162/1‑160 (MQ=255) cGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTaaa < 2:94160/160‑1 (MQ=255) gAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAggggg > 2:336836/1‑78 (MQ=255) aaCCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGG‑‑‑‑‑‑‑Tatc < 1:336848/78‑1 (MQ=255) ||||||| AGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATACATTCACAAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGG‑‑‑‑‑‑‑TATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATCCACTCTC > CP009273/481029‑481476 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |