Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,424,609 C→T 5.1% intergenic (‑167/+61) USA300HOU_RS12490 ← / ← USA300HOU_RS12495 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,424,6090CT 5.1% 536.4 / 8.6 175intergenic (‑167/+61)USA300HOU_RS12490/USA300HOU_RS12495hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (78/84);  new base T (8/3);  total (86/89)
Fisher's exact test for biased strand distribution p-value = 1.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 179 total aligned reads displayed.

TTTATTTAAATAACTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCATGTCGTCATCTTTCAATACGC  >  USA300TCH1516_ALE/2424469‑2424749
                                                                                                                                             |                                                                                                                                            
tttatttaAATAACTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTAc                                                                                                                                              >  2:922294/1‑141 (MQ=255)
     ttaAATAACTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACaaaaa                                                                                                                                         >  4:678288/1‑141 (MQ=255)
      taAATAACTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTGTAAAAAt                                                                                                                                        <  3:81518/141‑1 (MQ=255)
      taAATAACTTACATAATCAGAATAATACATGATGTTCAATAGGCCTGTCGATGATTCATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATAAAAAAAAACAAAAACACCCTTTTTAATTTTTGTAAAAAt                                                                                                                                        <  2:1225622/141‑1 (MQ=255)
       aaaTAACTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAAtt                                                                                                                                       >  3:704617/1‑141 (MQ=255)
           aaCTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTaaaa                                                                                                                                   >  1:1006007/1‑141 (MQ=255)
           aaCTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTaaaa                                                                                                                                   <  1:1372730/141‑1 (MQ=255)
            aCTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTaaaaa                                                                                                                                  >  3:280562/1‑141 (MQ=255)
            aCTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTaaaaa                                                                                                                                  >  3:667093/1‑141 (MQ=255)
             cTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCATTATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTaaaaaa                                                                                                                                 >  2:1506648/1‑141 (MQ=255)
              ttACATAATCATAATAATACTTGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTaaaaaaa                                                                                                                                <  1:1121947/141‑1 (MQ=255)
               tACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCTAAAACACCCTTTTTAATTTTTGTAAAAATTaaaaaggg                                                                                                                               <  1:880406/141‑4 (MQ=255)
                aCATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTTTTTTTTTTTATTATTCATTTATTCTATCAAAAACACCCTTTTTAATTTTTATAAAAATTaaaaaaatt                                                                                                                              >  4:428714/1‑139 (MQ=255)
                aCATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCATTTTTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAATTTaaaaaaaat                                                                                                                              >  2:1017917/1‑139 (MQ=255)
                aCATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGt                                                                                                                              >  2:791603/1‑141 (MQ=255)
                 cataatcataatAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTg                                                                                                                             >  2:758114/1‑141 (MQ=255)
                   taatcataatAATACATGATGTTTCATAGGCCTGTAGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCt                                                                                                                           >  1:1448222/1‑141 (MQ=255)
                    aaacataatAATACATGATGTTTCATAGGACTGACGATGATTGATTCACAATAGCACGTAATTTTTTTGTTTTTCAATATTATTCAAAAAAAAAAAAAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTc                                                                                                                          <  2:1110746/138‑1 (MQ=255)
                     atcataatAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTcc                                                                                                                         <  2:702526/141‑1 (MQ=255)
                      tcataatAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCt                                                                                                                        >  3:148751/1‑141 (MQ=255)
                      tcataatAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCt                                                                                                                        >  2:793335/1‑141 (MQ=255)
                        ataataataCATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTAAAAAAAATAAAAAAAGTGCTCCTac                                                                                                                      <  2:1370447/141‑1 (MQ=255)
                        ataataataCATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTAAAAAAAATAAAAAAAGTGCTCCTac                                                                                                                      <  4:628939/141‑1 (MQ=255)
                         taataataCATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTaca                                                                                                                     >  1:162607/1‑141 (MQ=255)
                          aataataAATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATATTAACAAAAATTAAAAAAAGTGCTCCTacac                                                                                                                    <  4:196970/141‑1 (MQ=255)
                             aataCATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATCTTATTCCTTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGc                                                                                                                 <  1:414468/141‑1 (MQ=255)
                               taCATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCtt                                                                                                               <  4:515493/141‑1 (MQ=255)
                               taCATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCtt                                                                                                               >  1:634866/1‑141 (MQ=255)
                                 cATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCttcc                                                                                                             >  2:174986/1‑139 (MQ=255)
                                 cATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGc                                                                                                             <  3:488745/141‑1 (MQ=255)
                                   tgatgTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCAt                                                                                                           >  1:1518130/1‑141 (MQ=255)
                                      tgTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTa                                                                                                        >  2:736505/1‑141 (MQ=255)
                                       gTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAg                                                                                                       >  1:1038782/1‑141 (MQ=255)
                                          tCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGTTTGCATGTAGaaa                                                                                                    >  2:182100/1‑141 (MQ=255)
                                           cATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAACTTAAAAAAAGTGCTCCTACACTGCTTGCATGTNGAAac                                                                                                   >  1:440690/1‑141 (MQ=255)
                                             tAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCGAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAacac                                                                                                 >  1:170114/1‑141 (MQ=255)
                                             tAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAacac                                                                                                 >  1:641343/1‑141 (MQ=255)
                                             tAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAacac                                                                                                 <  2:1215737/141‑1 (MQ=255)
                                             tAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAacac                                                                                                 <  3:58705/141‑1 (MQ=255)
                                             tAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAacac                                                                                                 >  1:641342/1‑141 (MQ=255)
                                             tAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAacac                                                                                                 <  1:699096/141‑1 (MQ=255)
                                             aaGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTAATCAATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAacac                                                                                                 <  2:449772/140‑1 (MQ=255)
                                              aGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTTTTTTTTTTTATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACt                                                                                                >  2:559472/1‑141 (MQ=255)
                                                 ccagTCGAAGAATAATTCACATTATCACGTTATTTTTTTGTTTTTCAATATTATTCATTTATTTCATCATAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCTTACACTGTTTTCATTTAGAAACACtttt                                                                                             >  2:988031/4‑141 (MQ=255)
                                                     tCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCAt                                                                                         >  2:1440149/1‑141 (MQ=255)
                                                       gatgatTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTg                                                                                       >  1:664778/1‑141 (MQ=255)
                                                       gatgatTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTg                                                                                       >  1:944064/1‑141 (MQ=255)
                                                        atgatTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGt                                                                                      <  1:1635809/141‑1 (MQ=255)
                                                         tgattgatTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTa                                                                                     <  2:475449/141‑1 (MQ=255)
                                                           attgattCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTa                                                                                     <  3:526038/139‑1 (MQ=255)
                                                             tgattCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAACGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGt                                                                                 <  1:821671/141‑1 (MQ=255)
                                                             tgattCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGt                                                                                 <  1:1004132/141‑1 (MQ=255)
                                                              gattTACAATAGCACGTGATTTTTTTGTTTTTCAATATTATCCATTTAGTCCATCAAAAACACCCTTTTTATTTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCAGTGTAATGtt                                                                                <  2:933884/141‑1 (MQ=255)
                                                              gattCACAATAGCACGTGATTTTTTTTTTTTTTTTTATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATTTAGAAACACTCTTTCATTTTAATGtt                                                                                >  4:493464/1‑141 (MQ=255)
                                                                ttCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTTTAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTAt                                                                              >  2:893635/1‑141 (MQ=255)
                                                                ttCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCGTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTAt                                                                              >  1:1304198/1‑141 (MQ=255)
                                                                ttCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTAt                                                                              <  2:1609580/141‑1 (MQ=255)
                                                                ttCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTAt                                                                              <  1:1384165/141‑1 (MQ=255)
                                                                ttCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTAt                                                                              <  3:692794/141‑1 (MQ=255)
                                                                ttCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTAt                                                                              <  1:21433/141‑1 (MQ=255)
                                                                 tCACAATAGCACGTGATTTTTTTGTTTTTTATTATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAACAAGTGCTCCTACACTGCTTGCATGTAGAAAAACTTTTTCATTGTAATGTTAtt                                                                             >  2:262326/1‑141 (MQ=255)
                                                                 tCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTAtt                                                                             <  1:248200/141‑1 (MQ=255)
                                                                       tAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTtctc                                                                       <  4:100851/141‑1 (MQ=255)
                                                                        aGCACGTGATTTTTTTGTTTTTTATTTTTTTTCATTTATTACATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAATTGCTACTACACTGCTTGCATGTAGAAACACTTTTTCATTTTGTTTTTATTCTTCTCg                                                                      >  4:397244/1‑141 (MQ=255)
                                                                          cACGTGATTTTTTTGTTTTTTAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAATAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATTTTATTCTTCTCgag                                                                    >  2:877870/1‑141 (MQ=255)
                                                                           aCGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCgaga                                                                   <  1:603252/141‑1 (MQ=255)
                                                                            cGTGATTTTTTTTTTTTTTTTTATTATTAAATTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAATTTCTCCTACACTGCTTGCATGCAGAAATATTTTTTTTTTTTAATTTTATTCTtctctatac                                                                  >  4:286499/1‑136 (MQ=255)
                                                                            cGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAg                                                                                                                               <  1:1236015/80‑1 (MQ=255)
                                                                            cGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGAc                                                                  >  1:396135/1‑141 (MQ=255)
                                                                            cGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGAc                                                                  <  2:36713/141‑1 (MQ=255)
                                                                             gtgtTTTTTTTGCTTCTCCATCTCATTCATTTATTACAACAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACa                                                                 <  2:1401885/141‑1 (MQ=255)
                                                                                  ttttttGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCt                                                            <  2:146211/141‑1 (MQ=255)
                                                                                      ttGTTTTTCAATATTATTCATTTATTTCATCAAATACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTa                                                        >  1:802238/1‑141 (MQ=255)
                                                                                        gttgttTNATATTAATTATTTATATTATTAAACACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTACTACACTGCCTGCACCTAGAACCACATTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGc                                                      <  2:1241990/141‑1 (MQ=255)
                                                                                        gTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGc                                                      >  1:1351120/1‑141 (MQ=255)
                                                                                         tttttCAATATTATTCATTTATTCCATCAAACACTCCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCa                                                     <  1:1578845/141‑1 (MQ=255)
                                                                                          ttttCAATATTATTCATTTATTCCATCGAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCat                                                    <  2:170114/141‑1 (MQ=255)
                                                                                          ttttAAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCat                                                    <  2:685742/141‑1 (MQ=255)
                                                                                             tCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATAtt                                                 <  4:159837/141‑1 (MQ=255)
                                                                                                 tattatTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGATACATACCTTTTAGCATATTAAGc                                             <  2:1474139/141‑1 (MQ=255)
                                                                                                    tattCATTTATTCCATCAAAAACACCCTTTTTTTTTTTTATTTAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACCTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCatg                                          >  4:316200/1‑141 (MQ=255)
                                                                                                     attCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCatgt                                         >  1:1123882/1‑141 (MQ=255)
                                                                                                      ttCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCatgta                                        >  1:1517178/1‑141 (MQ=255)
                                                                                                       tCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCatgtat                                       <  1:550687/141‑1 (MQ=255)
                                                                                                        cATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCatgtatg                                      >  1:1084640/1‑141 (MQ=255)
                                                                                                         aTTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAACACGTGCTCCCACCCTGCCTGCCTGTAGAAACAGTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCatgtatgt                                     <  3:493464/141‑1 (MQ=255)
                                                                                                             aTTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTaaa                                 <  2:655236/141‑1 (MQ=255)
                                                                                                              ttCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAAc                                <  3:412219/141‑1 (MQ=255)
                                                                                                               tCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACt                               <  2:227848/141‑1 (MQ=255)
                                                                                                                  aTCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACg                            >  3:218973/1‑141 (MQ=255)
                                                                                                                       aaaCACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCa                       >  1:732266/1‑141 (MQ=255)
                                                                                                                       aaaCACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTGTAGCATATTAAGCATGTATGTTAAACTACGGTTCa                       >  2:963171/1‑141 (MQ=255)
                                                                                                                        aaCACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCAt                      <  4:560498/141‑1 (MQ=255)
                                                                                                                         acacCCTTTTTAGGGGTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCATg                     <  2:1130391/141‑1 (MQ=255)
                                                                                                                           acCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCATgtc                   >  3:134917/1‑141 (MQ=255)
                                                                                                                            cccTTTTTAATTTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCATgtc                   <  2:126900/141‑1 (MQ=255)
                                                                                                                                    aaTTTTTACAAAAATTAAAAAAAGTGCTCCTACAGTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCCTGTATGTTAAACTACGGTTCCTGTCGTCACCttt          >  1:223074/1‑141 (MQ=255)
                                                                                                                                         tttACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCATGTCGTCATCTTTCAAt      >  2:1534752/1‑141 (MQ=255)
                                                                                                                                           tACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTAAGGTTTATTTCGTCATCTTTCAATAc    <  2:836976/141‑1 (MQ=255)
                                                                                                                                             cAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCATGTCGTCATCTTTCAATACGc  <  1:1506648/141‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                            
TTTATTTAAATAACTTACATAATCATAATAATACATGATGTTTCATAGGCCTGTCGATGATTGATTCACAATAGCACGTGATTTTTTTGTTTTTCAATATTATTCATTTATTCCATCAAAAACACCCTTTTTAATTTTTACAAAAATTAAAAAAAGTGCTCCTACACTGCTTGCATGTAGAAACACTTTTTCATTGTAATGTTATTCTTCTCGAGACATACCTTTTAGCATATTAAGCATGTATGTTAAACTACGGTTCATGTCGTCATCTTTCAATACGC  >  USA300TCH1516_ALE/2424469‑2424749

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: