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% 90.6 / ‑6.5 29intergenic (‑97/‑82)USA300HOU_RS00900/USA300HOU_RS00905hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base A (10/18);  minor base C (1/0);  total (11/18)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGA  >  USA300TCH1516_ALE/195148‑195420
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tttGTTTCTAGCTAAACTTACTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTCCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGACTTTTATCTAACTATTaaa                                                                                                                                      >  1:70607/1‑141 (MQ=255)
     ttCTAGCTACACTTGCTACGACAGATGCTTTATCCATAATGATAGCCCTCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaaaaaa                                                                                                                                 <  1:583741/141‑1 (MQ=255)
       cTAGCTAAACTTGCTACGACCGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAata                                                                                                                               >  1:482173/1‑141 (MQ=255)
                cTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAatat                                                                                                                      >  1:447457/1‑141 (MQ=255)
                 ttGCTACGACAGATTCTTTGTCCATAATGATAGCCCCCTATATTTATTTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAACTATTAAAAAAAACATCTTAATATc                                                                                                                     <  1:486696/141‑1 (MQ=255)
                 ttGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATc                                                                                                                     <  1:414379/141‑1 (MQ=255)
                   gCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAATTATTATAAAAAATATCTTAATATcat                                                                                                                   >  1:627396/1‑139 (MQ=255)
                               tCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATa                                                                                                       <  1:239627/141‑1 (MQ=255)
                                cTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATaa                                                                                                      >  1:655973/1‑141 (MQ=255)
                                               tAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAatat                                                                                       >  1:534351/1‑141 (MQ=255)
                                                  cccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtttt                                                                                    >  1:128945/1‑141 (MQ=255)
                                                                  ttatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtata                                                                    <  1:187743/141‑1 (MQ=255)
                                                                    ttttaCTTATACCCTAACATGATTTTTATACTCATATGCGAGATATTTCAGAGCATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAACCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagg                                                                  <  1:517440/140‑1 (MQ=255)
                                                                     tttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagga                                                                 <  1:52238/141‑1 (MQ=255)
                                                                        aCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCCACCATTGTTATAGGAGGt                                                              >  1:340009/1‑141 (MQ=255)
                                                                         cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTc                                                             <  1:764618/141‑1 (MQ=255)
                                                                         cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTc                                                             <  1:27223/141‑1 (MQ=255)
                                                                          ttATACCCTAATATGATTTTTATTCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGAAAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCt                                                            <  1:447144/141‑1 (MQ=255)
                                                                             taCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCttat                                                         <  1:625212/141‑1 (MQ=255)
                                                                               cccTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCttatta                                                       >  1:767618/1‑141 (MQ=255)
                                                                                  tAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAATTTTAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATg                                                    <  1:555996/141‑1 (MQ=255)
                                                                                  tAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAATTTGTATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATg                                                    <  1:555898/141‑1 (MQ=255)
                                                                                        gATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACatta                                              <  1:573815/141‑1 (MQ=255)
                                                                                         ttttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACattat                                             <  1:266527/140‑1 (MQ=255)
                                                                                         aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTCAAAAAATGTGCTTAATATCATTGTAATCCGATAAGAATTATATTAATATTTTTTCAACCATTGTTATATGAGGTCTTATTAATGACattat                                             >  1:331394/1‑141 (MQ=255)
                                                                                              tataCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTtta                                        <  1:6666/141‑1 (MQ=255)
                                                                                                taCTCTTTTAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTttatt                                      <  1:23607/141‑1 (MQ=255)
                                                                                                                       aGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTg               <  1:313432/141‑1 (MQ=255)
                                                                                                                        gAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGc              <  1:620935/141‑1 (MQ=255)
                                                                                                                              tATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAAc        >  1:408279/1‑141 (MQ=255)
                                                                                                                                    aaTATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAaaga  >  1:282163/1‑141 (MQ=255)
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TTTGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGA  >  USA300TCH1516_ALE/195148‑195420

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: ‑