| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | BS168_reference_genome | 1,317,152:1 | +GT | 100% | intergenic (+23/+5) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | BS168_reference_genome | 1,317,152 | 1 | . | G | 95.7% | 77.6 / ‑2.6 | 23 | intergenic (+23/+5) | phrA/yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (13/9); total (14/9) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-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. | |||||||||||
| * | BS168_reference_genome | 1,317,152 | 2 | . | T | 95.7% | 66.5 / ‑2.7 | 23 | intergenic (+23/+5) | phrA/yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (13/9); total (14/9) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-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. | |||||||||||
GTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑C‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAT > BS168_reference_genome/1317017‑1317264 || gTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGCTGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAggggtc < 1:110817/139‑4 (MQ=255)gTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATATCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAggggtc < 1:158367/139‑4 (MQ=255) cGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑G‑TCttttttattt > 5:184854/1‑135 (MQ=255) cTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCttt > 8:210539/1‑139 (MQ=255) ggTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAg < 4:248198/139‑1 (MQ=255) gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAg > 5:156905/1‑138 (MQ=255) gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc > 6:168241/1‑139 (MQ=255) aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc < 6:184854/139‑1 (MQ=255) cAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCAc < 2:139036/139‑1 (MQ=255) gAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCa < 8:280355/83‑1 (MQ=255) gAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCa > 7:280355/1‑83 (MQ=255) aaaCATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTAGCCACCAGCGGATCCGCATGGCCg > 8:282561/1‑138 (MQ=255) aaCATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGAt > 2:161629/1‑139 (MQ=255) aTTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTc > 8:258917/1‑139 (MQ=255) aTTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTc > 8:262571/1‑139 (MQ=255) tCATATTGCGGCAAGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCg < 2:159950/138‑1 (MQ=255) cATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATAGTCCGCTGAGAAGATCCACTTGCCACCAGCGGCTCCGCATGGCCGATTTCCGCt > 1:197371/1‑139 (MQ=255) tGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctc > 1:581/1‑139 (MQ=255) cGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCtt > 4:284341/1‑139 (MQ=255) cGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCGCTTCCAgg > 5:161764/1‑138 (MQ=255) tgatgCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg < 5:168241/139‑1 (MQ=255) atgCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt < 7:262571/139‑1 (MQ=255) atgCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt < 1:161629/139‑1 (MQ=255) tgCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt > 6:282036/1‑138 (MQ=255) tgCATAAAAAAAGACCCTTAGGGGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt < 7:258917/138‑1 (MQ=255) || GTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑C‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAT > BS168_reference_genome/1317017‑1317264 |
| 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: ‑ |