Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 195,286 T→A 100% intergenic (‑97/‑82) USA300HOU_RS00900 ← / → USA300HOU_RS00905 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE195,2860TA100.0% 87.9 / NA 26intergenic (‑97/‑82)USA300HOU_RS00900/USA300HOU_RS00905hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (14/12);  total (14/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACG  >  USA300TCH1516_ALE/195153‑195415
                                                                                                                                     |                                                                                                                                 
ttCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaaaaaa                                                                                                                            <  1:367910/141‑1 (MQ=255)
          aCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAata                                                                                                                  >  1:371597/1‑141 (MQ=255)
           cTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAatat                                                                                                                 >  1:425995/1‑141 (MQ=255)
              gCTACGACAGATTCTTTATCTATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAACATATCTTAATATCCt                                                                                                              <  1:343619/141‑1 (MQ=255)
                  cGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTa                                                                                                          >  1:197254/1‑141 (MQ=255)
                       gATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCg                                                                                                     >  1:429602/1‑141 (MQ=255)
                                     aaTGATAGCCCACGATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGt                                                                                       <  1:87067/141‑1 (MQ=255)
                                      aTGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTa                                                                                      >  1:445534/1‑141 (MQ=255)
                                       tGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTaa                                                                                     >  1:117418/1‑141 (MQ=255)
                                                ccTATATATATTTTTATTTACTTATAGCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTGTTATTTTTTc                                                                            <  1:340632/141‑1 (MQ=255)
                                                    tatatatGTTTATTTACTTATACCCTAACATGATTTTTTTACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAAcc                                                                        <  1:270905/141‑1 (MQ=255)
                                                    tatacatGCTTATTTACTTATACCCTAACATGATTTTTATCCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAAcc                                                                        <  1:157/141‑1 (MQ=255)
                                                           tgttttttaCTTATACCCTAATATGATTTTTATACCCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                                                                 <  1:154167/136‑1 (MQ=255)
                                                            tttagttaCTTATCCCCTAACATGATTTTTATACTCTTTGCAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat                                                                <  1:355327/141‑1 (MQ=255)
                                                              tatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTCATCCGTTAAGAATTATAGTAATTTTTTTTGAACCTTTGGTGTag                                                              >  1:204341/1‑141 (MQ=255)
                                                              tatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATAGATGTTAAAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCGACCATTGTTATag                                                              >  1:204326/1‑141 (MQ=255)
                                                                tttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGGTATagga                                                            >  1:145033/1‑141 (MQ=255)
                                                                         aCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCttatt                                                   >  1:76177/1‑141 (MQ=255)
                                                                              aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTACATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATAGTTATAGATGGGCTTATTAAtaa                                              >  1:272811/1‑139 (MQ=255)
                                                                              aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCGAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTTAACCATTGTTATATGAGGTCTTATTAATGa                                              >  1:244502/1‑141 (MQ=255)
                                                                               aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAc                                             >  1:143675/1‑141 (MQ=255)
                                                                                taTGATTTTTATACTCTTGAAAAATATATTTCACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACa                                            <  1:378249/140‑1 (MQ=255)
                                                                                          ataCTCTTTGAAAATATATTATACAGAATTTTATCTAAATATTAAAAAAAATATCTTAGTATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAGTGACATTATTTttat                                  >  1:281108/1‑141 (MQ=255)
                                                                                                tttGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAg                            <  1:204829/141‑1 (MQ=255)
                                                                                                       atatatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACaa                     <  1:387587/141‑1 (MQ=255)
                                                                                                               tACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGAtt             <  1:389808/141‑1 (MQ=255)
                                                                                                                          aTCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACg  <  1:196152/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                 
TTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACG  >  USA300TCH1516_ALE/195153‑195415

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑