| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,502,882:1 | +A | 100% | coding (1406/2106 nt) | melR_2 → | Melibiose operon regulatory protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,502,882 | 1 | . | A | 93.1% | 93.1 / 0.3 | 29 | coding (1406/2106 nt) | melR_2 | Melibiose operon regulatory protein |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base A (15/12); total (15/14) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.24e-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: Variant not supported by required number of reads on each strand. | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
TTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAG > USA300TCH1516_ALE/2502747‑2503017 | ttaaaaACAAAAATAAAGAAATTAAATATAGTGTGCCTGTTCAAGACTTTTTTTATAGGTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaa‑aa > 1:390769/1‑141 (MQ=255) aaaaaCAAAAATAAAGAAATTAAATCTAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCCTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaacaaa > 2:151390/1‑137 (MQ=255) aaaaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCTATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATAATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaa‑aaact > 1:27507/1‑138 (MQ=255) aaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaa‑aaactgc < 1:2866/141‑6 (MQ=255) tAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATc > 1:379073/1‑141 (MQ=255) gAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTAt > 1:33923/1‑141 (MQ=255) ttAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACt > 2:83794/1‑141 (MQ=255) ttAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATACAAAA‑AA‑CTGCAACACATCTTATCACt > 2:136091/1‑141 (MQ=255) aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTaaa < 1:254483/141‑1 (MQ=255) tataGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTaaaaa < 1:119495/141‑1 (MQ=255) aGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTatc > 2:227399/1‑141 (MQ=255) ttttAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGac < 1:254194/141‑1 (MQ=255) ttAGAAACTTATTCAACCGTGGAACAAGTTCATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGacac < 2:248354/141‑1 (MQ=255) tAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCAATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTCTCACTAAAAACCAACTATATCATCAGACTGCCACt > 1:11878/1‑141 (MQ=255) tAGAAACTTACGCAAACGTAGAACAAGTTTATCCTCTCAAGCAACGTCTTAAATTCCATTATGACTTTATTGAAAAAAAAAAAAAAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACt < 2:381135/141‑1 (MQ=255) aGAAACTTCTTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCCTAAATTCCATTATTTCTTAATTAAGGTGGAAAATTA‑AAATAA‑CTTGAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTc < 1:92721/141‑1 (MQ=255) aaCTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAtt < 1:55178/141‑1 (MQ=255) aTTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGaa > 1:344010/1‑141 (MQ=255) tCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa > 2:234880/1‑141 (MQ=255) aCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGta > 1:375603/1‑141 (MQ=255) gAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATAGAAAATTAAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGaa < 2:165295/141‑1 (MQ=255) aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAat > 1:665/1‑141 (MQ=255) aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAat > 2:387552/1‑141 (MQ=255) gTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACCCATTTTGAACAGTATAAGAAatttat > 1:82559/1‑141 (MQ=255) gTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTc < 1:162060/141‑1 (MQ=255) tCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCa > 1:256251/1‑141 (MQ=255) aTGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAgg < 1:207358/141‑1 (MQ=255) cAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGtat > 2:47300/1‑141 (MQ=255) tcttCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTatat < 2:66697/138‑1 (MQ=255) cTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATatcatc < 1:351095/141‑1 (MQ=255) gtAAGTTCCATTATTCTATTATTGTCATTGAAAATTCAAAA‑AA‑CTACGACTTTCCTTATCACTAAAAACCAACACTATCATCAAACTGACCCTCATTTTGAACAGTATAAGAAATTAATTTTAGATTCAGGTATAtcatca < 2:196302/140‑1 (MQ=255) ttATTGATATTGAAAATTCAAAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat > 2:184452/1‑141 (MQ=255) aaTTC‑AAA‑AACCTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAg < 1:302723/141‑1 (MQ=255) | TTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAA‑AA‑CTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAG > USA300TCH1516_ALE/2502747‑2503017 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |