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_ALE195,2860TA96.9% 152.9 / ‑3.2 48intergenic (‑97/‑82)USA300HOU_RS00900/USA300HOU_RS00905hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base A (24/22);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
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: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAG  >  USA300TCH1516_ALE/195150‑195422
                                                                                                                                        |                                                                                                                                         
tGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAaaaa                                                                                                                                       >  1:524733/1‑141 (MQ=255)
tGTTTCTAGCTAAACTTGCTACGAAAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGTAAATATATTTTACAGAATTTTATCTAAATATTTaaaa                                                                                                                                       >  2:47666/1‑141 (MQ=255)
 gTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaaaa                                                                                                                                      >  1:475176/1‑141 (MQ=255)
     cTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCTCCCTATATATATGTTTATTTACTTATATCCTATCATGTTTTTTATAGTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAATAAAAatt                                                                                                                                  >  1:38674/1‑140 (MQ=255)
     cTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAACAAata                                                                                                                                  >  1:106407/1‑141 (MQ=255)
      tAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTCTATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTTAAAATATCTTTTCCAGAATTTTTTTTAAATATTAATAAAAattt                                                                                                                                 >  2:617074/1‑139 (MQ=255)
        gCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATAACt                                                                                                                               >  2:396426/1‑141 (MQ=255)
             aCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAata                                                                                                                          <  2:190137/141‑1 (MQ=255)
             aCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAata                                                                                                                          <  2:532167/141‑1 (MQ=255)
               ttGCTACGACAGATTCTTTAACCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATc                                                                                                                        <  2:653361/141‑1 (MQ=255)
                 gCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCt                                                                                                                      >  1:409999/1‑141 (MQ=255)
                   tACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑Tg                                                                                                                   <  1:374707/141‑1 (MQ=255)
                      gACTGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAGAAGATTAAATTAATATCTTAATATCCT‑TGTaa                                                                                                                <  1:159869/141‑1 (MQ=255)
                           aTTCTTTATCCATAATGATAGCCCCCTATATATATGTTTCTTTCCTTATCACATTACGTGATTTTTATCCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGa                                                                                                           <  1:126358/141‑1 (MQ=255)
                               tttATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAg                                                                                                       <  1:87544/141‑1 (MQ=255)
                               tttATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAg                                                                                                       >  2:195658/1‑141 (MQ=255)
                                           gATAGCCCCCTATATATATGTTTATTTACTAATACCCTAAAATGATTTTTATAATCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑AGTAATACGATAAGGATTGTAGTAat                                                                                           >  1:195555/1‑141 (MQ=255)
                                                cccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATAtttt                                                                                      <  1:4693/141‑1 (MQ=255)
                                                 ccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAata                                                                                          >  1:26781/1‑136 (MQ=255)
                                                 ccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAata                                                                                          <  2:26781/136‑1 (MQ=255)
                                                  cccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATAtttttt                                                                                    <  2:20319/141‑1 (MQ=255)
                                                       aatatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAAcc                                                                               <  1:33919/140‑1 (MQ=255)
                                                              ggttatttaCTTATCCCCTAACATGAATTTTATACTCTTTGAAAATATATTTTACATAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                                                                        <  2:268202/139‑1 (MQ=255)
                                                                ttttttaCTTATACCCTAACATGATTTTTATAGTCGTTTAAAATATATTTTACAGAACTTTATATAAATATTAAAAAAAATATCTTAATATCCC‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtata                                                                      <  2:84778/138‑1 (MQ=255)
                                                                ttatgtaCTTAAAACCTAACATGATTTTTATACTCTTAGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtata                                                                      <  2:666281/141‑1 (MQ=255)
                                                                  attgaattATACCCTATCATCATTTTTATACTCATTAAAAATATATTTTACAGAATTGTATCAAAAAAAAAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagg                                                                    <  2:549664/135‑1 (MQ=255)
                                                                   tttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagga                                                                   >  1:360605/1‑141 (MQ=255)
                                                                   tttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagga                                                                   <  1:562642/141‑1 (MQ=255)
                                                                       cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAATAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCACCCATTGTTGTAGGAGGTc                                                               >  2:29993/1‑141 (MQ=255)
                                                                         tttgtccTATCATGATTGTTATTCTCTTTGAAAATATAGTTCGCACACTTTTATGTAAATATTAAAAAAAATATCTTCATATCCT‑TGTAATCCGATTAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtt                                                             <  2:567130/136‑1 (MQ=255)
                                                                            aCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCAGATATAAATTATAGTAATATTTTTTCAACCATTGTTCAAGGAGGTCttatt                                                          >  2:191395/1‑141 (MQ=255)
                                                                                 aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGa                                                     >  1:145790/1‑141 (MQ=255)
                                                                                    aTGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATTAAAATTATAGTAATATTTTTTTAACCATTGTTATAGGAGGTCTTATTAATGACat                                                  >  2:364662/1‑141 (MQ=255)
                                                                                                  ctTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATAGTTTtgatattaa                                    >  2:136332/1‑136 (MQ=255)
                                                                                                          atatatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACaa                            >  1:623726/1‑141 (MQ=255)
                                                                                                          atatatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACaa                            >  2:557128/1‑141 (MQ=255)
                                                                                                          atatatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTAAACCAATGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACaa                            >  1:624457/1‑141 (MQ=255)
                                                                                                           ttgagtttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAAt                           <  2:494821/136‑1 (MQ=255)
                                                                                                             tatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGCTAAGAATTATAGTAATATTTTCTCAGCCATTGTTATAGCAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCt                         <  2:274193/141‑1 (MQ=255)
                                                                                                                 ttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGAt                     >  2:626442/1‑141 (MQ=255)
                                                                                                                          tttATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACAATTGTTATAGGAGGTCTTATTACTGACATTATTTTTATTAGAAGCTAACCATCTTAAttttacgtaa            >  2:516567/1‑135 (MQ=255)
                                                                                                                          tttATCTAAATATTAAAAAAAATATCTT‑ATATTCTGTGTAATCCGAGAAAAAGTATAGTAATATTTTTTCAACCATTGATATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAAAAATATTGATTTTGCCTCa            >  2:276143/1‑141 (MQ=255)
                                                                                                                           ttATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCaa           <  1:348038/141‑1 (MQ=255)
                                                                                                                           ttATCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCaa           <  1:646474/141‑1 (MQ=255)
                                                                                                                             aTCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACg         <  2:360605/141‑1 (MQ=255)
                                                                                                                              tCTAAATATTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGa        >  2:655486/1‑141 (MQ=255)
                                                                                                                                  aaTATTAAAAAAAATATCTTAATATCCT‑TGTAATACGATCAGAATTATAGTAATATTTTTTCACCCATTGTTATAGGAGGTCTTATTAATTACATTATTTTTATTAGAAGCTAAGAATCTTGTTTTTGCATCAACGAaaga    >  2:657895/1‑141 (MQ=255)
                                                                                                                                   atatTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAaagaa   <  1:195658/141‑1 (MQ=255)
                                                                                                                                    tatTAAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACAATTGTTATAGGGGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTCATTTTGTATCCACGAaagaag  >  1:91839/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                         
TGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCT‑TGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAG  >  USA300TCH1516_ALE/195150‑195422

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: ‑