| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | NC_000913 | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,173,361 | 0 | C | . | 95.7% | 93.5 / ‑3.0 | 23 | pseudogene (918/1358 nt) | gatC | galactitol‑specific PTS enzyme IIC component |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (12/10); total (12/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.78e-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: 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. | |||||||||||
| * | NC_000913 | 2,173,362 | 0 | C | . | 95.7% | 94.2 / ‑2.9 | 23 | pseudogene (917/1358 nt) | gatC | galactitol‑specific PTS enzyme IIC component |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (12/10); total (12/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-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. | |||||||||||
CACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCC > NC_000913/2173226‑2173494 || cACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACATGATTACCCGGCACACAAACAGCAATTAGAATGGTGAGGGGGATAAAAATCAGGCTTGCCGATaccaccgccgtg > 1:654/1‑137 (MQ=255) gCACGGCGCCCGCCATCGCCCCGAAGAAGCCGAGGGTGCCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAATCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTccc < 2:322251/143‑1 (MQ=255) gCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGCATGTCCcagcag > 2:374566/1‑143 (MQ=255) gCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCGACGCCGGATc > 1:144396/1‑143 (MQ=255) cACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCaa > 1:295917/1‑143 (MQ=255) cACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCaa > 1:444598/1‑143 (MQ=255) gagaagaaGCCGACTGTGGCCAGTTCAGCAAACGGCAGCACCTGATTGCCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAACATCAGGCCTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg < 2:444813/141‑1 (MQ=255) tggCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTcc > 1:154672/1‑143 (MQ=255) cAAGACCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGa < 1:394163/143‑1 (MQ=255) aaCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCGAGCAGCAACGCCGGATCAAGGACA‑AACATGAACTCCTGACCGCCGATCtc > 2:101417/1‑142 (MQ=255) aCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTc < 1:368349/143‑1 (MQ=255) ggCAGCACCTGATCACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGc < 1:189402/143‑1 (MQ=255) ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGa < 1:383937/143‑1 (MQ=255) cGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCTGCAGCAACGCCAGAT‑AACGCAACATTTTGAACTCCTGACCCCCGAACTTCGCCTGTAAACGACTACGAg > 2:307131/1‑143 (MQ=255) cGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCCGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGACCTTCGCCTGTAAACGACTAcaac > 2:181866/1‑140 (MQ=255) ggCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGTTGGTGC‑‑CCCCACCATATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGc < 1:513505/143‑1 (MQ=255) cacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGc > 1:106687/1‑143 (MQ=255) aaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTa < 1:24220/143‑1 (MQ=255) ggcgAGTGGGAGAACGCTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAAc < 2:160941/140‑1 (MQ=255) gAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGGCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGAGTACGAGCCTGCTTAGCGATGGGCGGTAAAccat > 1:153261/1‑143 (MQ=255) aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAAc > 1:112292/1‑100 (MQ=255) aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAAc < 2:112292/100‑1 (MQ=255) aTCAGGCTTGCCGATACCA‑‑CCGCCGTAGGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGttt < 2:97896/143‑1 (MQ=255) tGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGCGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCAccc > 2:232069/1‑143 (MQ=255) || CACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCA‑ATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCC > NC_000913/2173226‑2173494 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |