| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_004302 | 1,914 | 0 | T | C | 23.3% | 198.9 / 69.9 | 235 | intergenic (‑54/+7) | r1tp02/rro | ORF2/Repressor protein |
| Reads supporting (aligned to +/- strand): ref base T (4/121); new base C (0/38); total (4/231) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.74e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
Only 100 of 312 total aligned reads displayed.
GGAGTTTTTCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATCAATTTCTACTTTGACAGCTTGCCCAATCACAGCTGCTGGATTGTCTTGTG > NC_004302/1841‑1979 | ggAGTTTTTCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGt‑a‑tc < 1:10096233/75‑2 (MQ=255) gAGTTTTTCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGt‑a‑ttc < 1:7675381/75‑3 (MQ=255) aGTTTTTCCA‑‑TTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCat‑a‑ttccag < 1:3863800/75‑6 (MQ=255) gTTTTTCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGt‑a‑tccca < 1:12624204/75‑5 (MQ=255) ttttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCat‑a‑tcttaca < 1:13065304/75‑7 (MQ=255) ttttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGt‑a‑tgcatcc < 1:11000863/75‑7 (MQ=255) ttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCTt‑a‑t‑acagacgc < 1:9963534/75‑8 (MQ=255) ttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGt‑a‑t‑acgatgtt < 1:15898438/75‑8 (MQ=255) ttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atcattct < 1:9397737/75‑7 (MQ=255) ttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attagggt < 1:8239680/75‑6 (MQ=255) ttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCG‑‑A‑T‑Attaatact < 1:2520378/75‑7 (MQ=255) ttCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑‑TGCTCGT‑A‑G‑Attcgctat < 1:10714644/75‑7 (MQ=255) ttcATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑TTTTAAtaa < 1:17583877/73‑3 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACTTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTGATtac < 1:6884412/75‑2 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atgttcgat < 1:5501837/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atggtagtc < 1:12752374/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atcttcgtt < 1:584728/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atcttaaat < 1:8063464/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atctgagtg < 1:8516673/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atctgaaga < 1:5766811/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atccttcca < 1:2906542/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atcaggtga < 1:14932944/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atcacataa < 1:9185220/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atatgtttc < 1:1665455/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atatctact < 1:4569056/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atacccagt < 1:1890591/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑a‑t‑atacatata < 1:1266342/75‑8 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑AGT‑ATTTactc < 1:1813685/75‑4 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑TCATTTAAta < 1:6522532/75‑2 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑tttttcaaa < 1:3433349/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑tttttacac < 1:4524279/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ttttcaaat < 1:961951/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑TTTTaccct < 1:16972785/75‑5 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑TTTTTAttc < 1:5725545/75‑2 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑Ctttgtatg < 1:2237996/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑Atttttctc < 1:5923431/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑Attcgtttg < 1:17251982/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑Attaccacc < 1:15373380/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑G‑Attgggttc < 1:12027488/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attttccaa < 1:4039201/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attgattgc < 1:16357654/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attgaccct < 1:6158732/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attcttaca < 1:14486924/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attctaact < 1:4495976/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attcctttg < 1:13873640/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attatctaa < 1:11310938/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attacgctc < 1:16131063/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑ATTCAAttc < 1:503020/75‑2 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑A‑Attttccct < 1:6707537/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑A‑Atttctcca < 1:13161531/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑A‑Attcccggg < 1:17422441/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑A‑Attcaggaa < 1:3473159/75‑7 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTatctcc < 1:7293055/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTagacaa < 1:3979152/75‑6 (MQ=255) tCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTAAtaac < 1:10004310/75‑4 (MQ=255) ccATTTTTCATAATGTTTTATATTTTCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑ACT‑Atttcacg < 1:12211333/75‑5 (MQ=255) ccATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Atttctcagt < 1:15155992/75‑7 (MQ=255) ccATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Attctttgtc < 1:8459719/75‑8 (MQ=255) ccATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑A‑Attttcaatc < 1:7360618/75‑7 (MQ=255) ccATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑A‑Attaaagctc < 1:12338121/75‑8 (MQ=255) ccATTTTTCATAATG‑TTTATA‑TTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTaactcact < 1:14293644/75‑7 (MQ=255) ccATTTTTCATAATG‑TTT‑TATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGTAA‑T‑Atttgtccca < 1:15638923/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAGCGAGAATCAAGACA‑TTGCTCGT‑A‑C‑CTTTAATtaaa < 1:1382537/75‑3 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGTAA‑T‑Atttcaagtc < 1:8753120/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑ACT‑Atttccacaa < 1:542447/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ttttctattaa < 1:11867631/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑aattaatttgc < 1:745178/75‑4 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑Atttttgccat < 1:5139424/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑Attttcgaccc < 1:5290/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTagacctt < 1:9252847/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTGAttcca < 1:2442813/75‑4 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ACTTagatgtt < 1:7998/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑AATTacgtctt < 1:12871492/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑‑TTTaacacaat < 1:4918688/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑‑TTTaaactcca < 1:8645618/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑TTTTAAtattt < 1:10545519/75‑5 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Atttcctcaag < 1:190992/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑Atttcaacatc < 1:13473149/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑C‑ATTAAAttcct < 1:13566217/75‑4 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTatcatccc < 1:8974213/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTagccctct < 1:13976655/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTagatagtc < 1:3720388/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTaccacacg < 1:2594509/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTacatggaa < 1:14753197/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTacacctca < 1:11085690/75‑8 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTaacccgct < 1:3102163/75‑7 (MQ=255) cATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑‑‑ATTTAAtaccct < 1:11692078/75‑6 (MQ=255) aTTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑G‑ATTAAAtcatct < 1:10241694/75‑6 (MQ=255) ttttCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACATTTGCTCGT‑A‑T‑ATTTCAttcccca < 1:2992375/75‑6 (MQ=255) tCATAATG‑TTTTTATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAataatagaactg < 1:8890932/75‑7 (MQ=255) tAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATcctcaa < 1:6285408/75‑6 (MQ=255) g‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAAT‑AAttttccag < 1:430500/75‑6 (MQ=255) tttATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑ATT‑ATTTAATTATAAATCAAttttcct < 1:17047457/75‑5 (MQ=255) tttATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAAT‑AATTTcctacc < 1:1374034/75‑6 (MQ=255) tCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATCAATTTCCACttgtaacag < 1:13312654/75‑8 (MQ=255) ccTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATCAATTTCTACTTTGACAGCttatct < 1:15987989/75‑5 (MQ=255) ttttAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATCAATTTCTACTTTGACAGCTTGccttaccaa < 1:4702057/75‑8 (MQ=255) tttAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATCAATTTCTACTTTGACAGCTTGCTCAATcgcc < 1:7881229/75‑4 (MQ=255) tttAACGAGAATCAAGACA‑TTGCCCGT‑A‑T‑ATTTAATTATAAATCAATTTCTACTTTGACAGCTTGccccaaatca < 1:6450697/75‑8 (MQ=255) ttAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATCAATTTCTACTTTGACAGCTTGCCCAAGcactg < 1:6612747/75‑3 (MQ=255) | GGAGTTTTTCCATTTTTCATAATG‑TTTATATTTCCTAACCTAGCTTTTAACGAGAATCAAGACA‑TTGCTCGT‑A‑T‑ATTTAATTATAAATCAATTTCTACTTTGACAGCTTGCCCAATCACAGCTGCTGGATTGTCTTGTG > NC_004302/1841‑1979 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |