| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,613,762 | T→C | 100% | intergenic (‑31/‑37) | scpA ← / → USA300HOU_RS08000 | Segregation and condensation protein A/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 1,613,762 | 0 | T | C | 99.0% | 81.6 / ‑6.6 | 25 | intergenic (‑31/‑37) | scpA/USA300HOU_RS08000 | Segregation and condensation protein A/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (13/11); minor base G (1/0); total (14/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| 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: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
TAAATATCTATTTCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAA > USA300TCH1516_ALE/1613625‑1613894 | tAAATATCTATTTCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGaa > 1:136899/1‑141 (MQ=255) aaaTATCTATTTCAAATTTCTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGaaa > 1:237104/1‑141 (MQ=255) ttttGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAAt > 2:233111/1‑141 (MQ=255) gATAAGATGCAGCAATCAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATCATATCTACTTCGGATTGCGTCATATGTGCATAATTCTCTCAAAAATTATAGCAGGAAAATAACTTACTTTTAAATTgggg > 2:134960/1‑141 (MQ=255) aTGAAGCAATAAAACTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCCCCCAAATATTATATCACTAAAATAACTTACTTTTAAATTGGGGTGATaa < 1:233111/141‑1 (MQ=255) tGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAAc < 2:388561/141‑1 (MQ=255) gcagcaATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACa < 2:209275/141‑1 (MQ=255) gcagcaATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACa < 2:201834/141‑1 (MQ=255) gaaaTAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaaaa < 1:176214/139‑1 (MQ=255) aTACATCTAATGGCCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc < 2:258962/141‑1 (MQ=255) aTAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc > 1:314706/1‑141 (MQ=255) ccATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATa > 2:257317/1‑141 (MQ=255) ttCATCCATAAGATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATAc < 1:16756/141‑1 (MQ=255) cTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCt < 1:40440/141‑1 (MQ=255) tGCGTCATATGTGCATGAGTCTCTAAGATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACCTTATTTCCTATGTCAt < 2:97829/141‑1 (MQ=255) gCGTAATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATg > 1:269112/1‑141 (MQ=255) gTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGAc < 1:39860/141‑1 (MQ=255) tCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACa > 1:327048/1‑141 (MQ=255) atGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACAtttt < 2:314706/141‑1 (MQ=255) cATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTagaag > 1:184379/1‑141 (MQ=255) tctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATgg > 2:33714/1‑141 (MQ=255) aaTATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGc > 2:147027/1‑141 (MQ=255) ttatAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGTAGATGCATGGAAAGCTGaa > 1:314914/1‑141 (MQ=255) ttatAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGaa > 1:36927/1‑141 (MQ=255) ttatAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGaa > 2:308012/1‑141 (MQ=255) | TAAATATCTATTTCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAA > USA300TCH1516_ALE/1613625‑1613894 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |