| 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 | 95.0% | 141.4 / 0.3 | 40 | intergenic (+23/+5) | phrA/yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base G (22/16); total (23/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-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 | 95.0% | 115.4 / 0.3 | 40 | intergenic (+23/+5) | phrA/yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base T (22/16); total (23/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-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. | |||||||||||
GCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑C‑TTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACA > BS168_reference_genome/1317024‑1317268 || gCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑G‑TCtt‑tttt < 8:330558/138‑1 (MQ=255) cGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACACCAAACACAGAAGGGAAAACATTTCATATTTCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑G‑TCtt‑ttttatt > 6:301653/1‑135 (MQ=255) cTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCttt > 1:242948/1‑139 (MQ=255) tACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCtttt < 4:146500/137‑1 (MQ=255) cTCAGGTGATGGGTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATc < 2:158396/138‑1 (MQ=255) aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGt > 4:80420/1‑137 (MQ=255) aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGt < 4:300802/137‑1 (MQ=255) ggTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAg < 4:190566/139‑1 (MQ=255) gTGATGGTTCATGCAGGTGCAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGc > 5:337361/1‑139 (MQ=255) gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGt < 3:31640/135‑1 (MQ=255) gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGt > 4:31640/1‑135 (MQ=255) aTGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCt > 3:346949/1‑137 (MQ=255) aTGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTc < 1:306027/138‑1 (MQ=255) aTGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCATTTATCGTCAGCTCa > 4:182061/1‑139 (MQ=255) gTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCaga < 3:80420/138‑1 (MQ=255) tCATGCAGGTGAAACAGCACACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACACTTAGGGGTC‑TTTTATATTTCTTCAGCTTCAATTCTTTATTCGACAGCTCat > 5:171929/1‑134 (MQ=255) aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGAtg > 1:173576/1‑138 (MQ=255) aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc > 5:75905/1‑139 (MQ=255) aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc > 4:281423/1‑139 (MQ=255) aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc > 8:272130/1‑139 (MQ=255) gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCCGCTCAGAAGATCCACTTg > 6:85236/1‑139 (MQ=255) gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAg > 8:276338/1‑122 (MQ=255) gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAg < 7:276338/122‑1 (MQ=255) gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTg > 8:296970/1‑139 (MQ=255) aaaCAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGcca > 7:302376/1‑139 (MQ=255) gAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCa > 4:309450/1‑139 (MQ=255) gAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGcc < 4:43155/139‑1 (MQ=255) atatTGCGGCAAGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt < 6:189322/138‑1 (MQ=255) tGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctc > 5:320724/1‑139 (MQ=255) gCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctct > 5:89846/1‑139 (MQ=255) gCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGAGTTCCGCTGCctct > 8:83910/1‑139 (MQ=255) aTCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAAt < 2:242948/139‑1 (MQ=255) aCATGATGCATTAATATAGTCACTTAGGGGTCTTTTT‑TATTTCTTCTGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCAGTTGCCACCATCGGATCCTCATGGCCGATTTCCTCTTACTCTTCCTGTGTATATGCt < 2:20590/139‑1 (MQ=255) cATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCtt < 3:281423/139‑1 (MQ=255) cATGATGCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCGCTTCCAGTGAATCTGCtt < 6:337361/139‑1 (MQ=255) gatgCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCGCTTCCAGTGAATCTGCTTCGa > 7:130261/1‑139 (MQ=255) tgCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt < 5:301653/138‑1 (MQ=255) tgCATAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGGCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCTTGGCCGAGTTCCGCTGCCTGTTGCAGTGATTCTGATTCGAt > 3:195941/1‑138 (MQ=255) aTAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa < 6:75905/139‑1 (MQ=255) tAAAAAAAGACCCTTAGGGGTCTTTTT‑TATTTCTTCAGCTTCCATTGTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa > 3:237216/1‑138 (MQ=255) || GCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑C‑TTTT‑TATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACA > BS168_reference_genome/1317024‑1317268 |
| 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: ‑ |