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% 109.3 / NA 34intergenic (‑97/‑82)USA300HOU_RS00900/USA300HOU_RS00905hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (23/11);  total (23/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGA  >  USA300TCH1516_ALE/195152‑195416
                                                                                                                                      |                                                                                                                                   
tttCTAGCTAAACTTGCTACGCCAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAaaaaaa                                                                                                                               <  1:460095/141‑1 (MQ=255)
           aCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAata                                                                                                                    >  1:310996/1‑141 (MQ=255)
              tGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTATATGTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATct                                                                                                                 >  1:252455/1‑140 (MQ=255)
               gCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCt                                                                                                                >  1:73322/1‑141 (MQ=255)
                           tCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATa                                                                                                    <  1:465869/141‑1 (MQ=255)
                            cTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCATTGTAATCCGATaa                                                                                                   >  1:79614/1‑141 (MQ=255)
                                  ccATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATta                                                                                             <  1:207340/141‑1 (MQ=255)
                                   cATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAttgt                                                                                            >  1:303995/1‑139 (MQ=255)
                                       aTGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTa                                                                                        >  1:88702/1‑141 (MQ=255)
                                          aTAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAata                                                                                     >  1:408553/1‑141 (MQ=255)
                                            aGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCTATAAGAATTATAGTAAAAtt                                                                                   >  1:145486/1‑141 (MQ=255)
                                                   tatatataTGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                                                                            >  1:556809/1‑141 (MQ=255)
                                                     tatatatGTTTATTTACTTACACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATGAGAATTATAGTAATATTTTTTCAAcc                                                                          >  1:348886/1‑141 (MQ=255)
                                                      atatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCa                                                                         >  1:457752/1‑141 (MQ=255)
                                                        atatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCAtt                                                                       <  1:352947/141‑1 (MQ=255)
                                                         tatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTTTAGTAATATTTTTTCAACCATTg                                                                      >  1:226938/1‑141 (MQ=255)
                                                              ttatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat‑a                                                                <  1:304285/141‑1 (MQ=255)
                                                                       tataCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCtt                                                       <  1:528030/141‑1 (MQ=255)
                                                                         taCCCTAACATGATTTTTATACTCTTTGAAAATATATTATACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCttat                                                     >  1:369243/1‑141 (MQ=255)
                                                                                aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGAc                                              <  1:245806/141‑1 (MQ=255)
                                                                                    gATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGTGGTCTTATTAATGACattt                                          >  1:461991/1‑140 (MQ=255)
                                                                                     aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTACAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACattat                                         >  1:380464/1‑141 (MQ=255)
                                                                                       ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTAttt                                       >  1:394920/1‑141 (MQ=255)
                                                                                       ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTAttt                                       >  1:104623/1‑141 (MQ=255)
                                                                                       ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTAttt                                       >  1:469462/1‑141 (MQ=255)
                                                                                       ttttATACTCTTTGAAAATATATTTTAAAGAATTTTATCTAAATATTAAAAACAATATCTTAATATTCTTGTACTCCGATAAGAATTATAGTAATATTTTTTCAACCCTTGTTGTCAGGA‑GTCTTATTAGTAACATTAttt                                       >  1:176302/1‑141 (MQ=255)
                                                                                             aCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTttatta                                 >  1:39650/1‑141 (MQ=255)
                                                                                                  ttGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATTTCTTTATTTCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGc                            <  1:272160/141‑1 (MQ=255)
                                                                                                     aaaaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTaa                         >  1:49965/1‑141 (MQ=255)
                                                                                                           tatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGGATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCt                   <  1:259302/141‑1 (MQ=255)
                                                                                                              tttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGa                >  1:402294/1‑141 (MQ=255)
                                                                                                                    gAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGc          <  1:154097/141‑1 (MQ=255)
                                                                                                                    aaaTTTCATCTAAATATTAAAAAAAATAGCCTAATATCGTTGGAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTCTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGc          <  1:194731/140‑1 (MQ=255)
                                                                                                                            tCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTACCAATCTTGATTTTGCATCACCGa  >  1:96528/1‑141 (MQ=255)
                                                                                                                                      |                                                                                                                                   
TTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGA  >  USA300TCH1516_ALE/195152‑195416

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑