| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | NC_002947 | 4,336,532:1 | +C | 100% | coding (683/885 nt) | PP_3811 ← | LysR family transcriptional regulator |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,336,532 | 1 | . | C | 77.8% | 38.4 / 9.2 | 18 | coding (683/885 nt) | PP_3811 | LysR family transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base . (2/2); new base C (4/9); total (7/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.84e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
TACACCGCCGACAGCTGCAGCGCGGGCGGGCGCCACTCATCCAGAACCGTCACCAGTTGCCCCTCCGCCAACGCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑G‑CCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATAAGGCAGGCAATCATGCGCGGCGAGCTCATCCG > NC_002947/4336406‑4336673 | tACACCGCCGACAGCTGCAGCGCGGGCGGGCGCCACTCATCCAGAACCGTCACCAGTTGCCCCTCCGCCAACGCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCAt < 6:365315/149‑1 (MQ=255) gcgggcggGCGCCACTCATCCAGAACCGTCACCAGTTGCCCCTCCGCCAACGCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCgg < 1:7666/149‑1 (MQ=255) cTCATCCAGAACCGTCACCAGTTGCCCCTCCGCCAACGCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGcc < 1:63891/149‑1 (MQ=255) aCCGTCACCAGTTGCCCCCCCGCCAACGCCTGCCCAACGATAAAGTTAGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCTCCCGGTCACCTGAATTGCCTTGGTTTTGc < 3:44519/149‑1 (MQ=255) gTCAACAGTTGCCCCTCCGCCAACGCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCAc < 1:317136/149‑1 (MQ=255) cAACGCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACGCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCACCGCCCCATTGTTAGCCCGCATGCGCCCGGGCACCTGAATTGCCTGGGTTTGTCCACCATTGTGGAATTGACCCTGc > 6:23365/1‑149 (MQ=255) gCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACCCCCATCCCGGGAATCGCA‑GCCCCC‑CCGCCGCAACTCGCGCGTGTTCGCCCGCCTGCGCCCGGTCACCTGAATTGCCTGGGTTTTGGGACCGTTGTGGAATTGGAACTGCACCt > 8:11786/1‑149 (MQ=255) ccAACGATAAAGGTCGGCAGGTAAGTGACACCCATCCCAGCAATCACA‑GAAACC‑CCGCAGCAAATCCAAAAAGTTCGCCCGCAAGGGCACGGTGAGCGGAATTGCCAGGGGTTTGCCACGGGTGTGGAATTGCCACGGCACCTGCcgc > 8:54143/1‑148 (MQ=255) taaGGTCGGCAGGTAAGTGACCCCCATACCGGCAATCGCA‑G‑CCCCACCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGAACCTGCcgc < 5:243015/139‑1 (MQ=255) aaaGGTCGGCAGGTAAGTGAGGCCCGGCCCGGCAGTCGGG‑GCCCCC‑CCGCAGCAAGACGCCAAAGTACGGCCCCGGGGGCCCGGTCACCGGAATTGGGTGGGGTTTGAGAGCTTTGTGGAAATGCCGCGGCACCTGCCGCGCATGccc > 2:271702/1‑148 (MQ=255) aGGTCGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATa < 5:23365/149‑1 (MQ=255) cGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑C‑CCCC‑CCGCAGCAACTCGCCAATGTTCGCCCGCATGCGCCCGGGCACCTGAAATGCCTGGGTTTTGCCACCTTTGTGGCATTGCCACTGCACCTGCCGCGAATGCCCATAagg > 3:52113/1‑147 (MQ=255) actgccccccATCCCCCCAATCGCACC‑CCCC‑CCCCAGCAACTAGCCATTGTTCGCCCGCATTCGCTCGGTTACCTTAATTGGCTGGGTTTTTCCACCTTTTTGGAATTTCCACTGCACCTTCCGCGAATGCCCATAAGGCAGGCAATCa < 7:54143/144‑1 (MQ=255) aGTGACCCCCATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATAAGGCAGGCAATc < 7:11786/148‑1 (MQ=255) ccccATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATAAGGCAGGCAATCATGcgcg > 1:175441/1‑149 (MQ=255) ccccATCCCGGCAATCGCA‑G‑CCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATAAGGCAGGCAATCATGCgcgg > 7:299054/1‑149 (MQ=255) cccATCCCGGCAATCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCTCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATAAGGCAGGCAATCATGCgcgg < 2:175441/149‑1 (MQ=255) aTCGCA‑GCCCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATAAGGCAGGCAATCATGCGCGGCGAGCTCATCCg < 5:311451/149‑1 (MQ=255) | TACACCGCCGACAGCTGCAGCGCGGGCGGGCGCCACTCATCCAGAACCGTCACCAGTTGCCCCTCCGCCAACGCCTGCCCAACGATAAAGGTCGGCAGGTAAGTGACCCCCATCCCGGCAATCGCA‑G‑CCCC‑CCGCAGCAACTCGCCATTGTTCGCCCGCATGCGCCCGGTCACCTGAATTGCCTGGGTTTTGCCACCTTTGTGGAATTGCCACTGCACCTGCCGCGAATGCCCATAAGGCAGGCAATCATGCGCGGCGAGCTCATCCG > NC_002947/4336406‑4336673 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |