Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*1298,9620CT63.8% 62.3 / 65.2 69intergenic (–/–)–/––/–
Reads supporting (aligned to +/- strand):  ref base C (13/12);  new base T (22/22);  total (35/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.19e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GGCAGATGATGTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACGGGGGCGA  >  129/8864‑9062
                                                                                                  |                                                                                                    
ggCAGATGATGTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTa                                                                                                    >  1:1448597/1‑101 (MQ=255)
  cAGATGATGTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACg                                                                                                  <  2:190497/101‑1 (MQ=255)
  cAGATGATGTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACg                                                                                                  <  2:432845/101‑1 (MQ=255)
     atgatgTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGtt                                                                                               >  1:492579/1‑101 (MQ=255)
     atgatgTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGtt                                                                                               <  2:1235057/101‑1 (MQ=255)
      tgatgTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTg                                                                                              >  2:1110911/1‑101 (MQ=255)
       gatgTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGc                                                                                             >  2:587641/1‑101 (MQ=255)
        atgTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGct                                                                                            <  2:1426443/101‑1 (MQ=255)
        atgTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGct                                                                                            <  2:881326/101‑1 (MQ=255)
         tgttgtCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGccc                                                                                           >  1:773189/1‑99 (MQ=255)
          gttgtCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGctct                                                                                          <  2:935100/101‑1 (MQ=255)
          gttgtCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGAGATGCTGGCGGACCTTATCCGGCTTACGGTTGctct                                                                                          >  1:23385/1‑101 (MQ=255)
             gtCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCca                                                                                       <  2:278534/101‑1 (MQ=255)
             gtCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCca                                                                                       <  1:1110916/101‑1 (MQ=255)
               cAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCcagc                                                                                     >  1:1643391/1‑101 (MQ=255)
               cAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCcagc                                                                                     >  2:294040/1‑101 (MQ=255)
                aaaGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCcagcc                                                                                    <  2:339899/101‑2 (MQ=255)
                aaaGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCcagcc                                                                                    >  1:844385/1‑100 (MQ=255)
                aaaGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGGCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCcagcc                                                                                    >  2:429596/1‑100 (MQ=255)
                 aaGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCcagccg                                                                                   >  1:1094193/1‑99 (MQ=255)
                    agTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCcagccgggt                                                                                >  1:1003871/1‑96 (MQ=255)
                      tATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTg                                                                              <  2:890346/101‑1 (MQ=255)
                      tATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTg                                                                              <  2:1355847/101‑1 (MQ=255)
                       aTGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTgg                                                                             >  2:1524820/1‑101 (MQ=255)
                         gCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGAt                                                                           <  1:1490693/101‑1 (MQ=255)
                              gtTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGc                                                                      >  2:987881/1‑101 (MQ=255)
                                 aaTGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGtt                                                                   >  2:1507328/1‑101 (MQ=255)
                                 aaTGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGtt                                                                   >  2:1677966/1‑101 (MQ=255)
                                    gTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTat                                                                <  2:1685827/101‑2 (MQ=38)
                                    gTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTat                                                                <  1:1304254/101‑2 (MQ=38)
                                    gTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTat                                                                <  1:97046/101‑2 (MQ=38)
                                    gTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTat                                                                >  2:1193806/1‑100 (MQ=255)
                                      cATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTAtgc                                                              <  2:772590/101‑1 (MQ=38)
                                        tttCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTAtgccg                                                            <  1:1131258/101‑1 (MQ=38)
                                           cGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCAt                                                         <  1:376689/101‑1 (MQ=38)
                                           cGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCAt                                                         >  2:1690194/1‑101 (MQ=38)
                                             atgatACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATcc                                                       >  1:1241266/1‑101 (MQ=38)
                                             atgatACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATcc                                                       <  2:209255/101‑1 (MQ=38)
                                                atACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATCCgac                                                    >  2:644406/1‑99 (MQ=38)
                                                 tACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATCCGACa                                                   <  2:1448591/101‑1 (MQ=37)
                                                  aCCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATCCGACag                                                  <  1:1350347/101‑2 (MQ=37)
                                                   ccGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATCCGACagc                                                 >  2:1012131/1‑99 (MQ=37)
                                                   ccGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGCTGGATAAGGCGTTTATGCCGCATCCGACagc                                                 >  1:438706/1‑99 (MQ=37)
                                                      tGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATCCGACagctat                                              <  2:431478/101‑6 (MQ=37)
                                                       cgacagctatCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCa                                             <  1:723077/92‑1 (MQ=255)
                                                        gacagctatCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCAc                                            >  2:1368357/9‑101 (MQ=255)
                                                         gACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCTTACGGTTGCTCTCCAGCCGGGTTGGATAAGGCGTTTATGCCGCATCCGACagctatcgc                                           >  1:501838/1‑93 (MQ=37)
                                                           agctatCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGt                                         >  1:1512805/6‑101 (MQ=255)
                                                           agctatCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGt                                         >  2:1546468/6‑101 (MQ=255)
                                                            gctatCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGtt                                        <  2:501833/97‑1 (MQ=255)
                                                               atCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAg                                     <  2:350972/100‑1 (MQ=255)
                                                                tCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAgg                                    <  2:1643385/101‑1 (MQ=255)
                                                                  gCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCg                                  <  1:221557/101‑1 (MQ=255)
                                                                     ggATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTca                               >  2:1050241/1‑101 (MQ=255)
                                                                      gatgcgatgcTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTcac                              >  1:1437736/1‑101 (MQ=255)
                                                                      gatgcgatgcTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTcac                              >  1:291812/1‑101 (MQ=255)
                                                                        tgcgatgcTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACAt                            <  1:1368614/101‑1 (MQ=255)
                                                                         gcgatgcTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATc                           >  1:364431/1‑101 (MQ=255)
                                                                          cgatgcTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATcc                          >  2:272686/1‑101 (MQ=255)
                                                                          cgatgcTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATcc                          >  1:74291/1‑101 (MQ=255)
                                                                           gatgcTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCg                         <  2:438701/101‑1 (MQ=255)
                                                                               cTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCtgttgt                     <  1:1012944/101‑1 (MQ=255)
                                                                                    gcATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCt                <  1:1546474/101‑1 (MQ=255)
                                                                                    gcATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCt                <  1:823963/101‑1 (MQ=255)
                                                                                     cATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTg               >  2:1623207/1‑101 (MQ=255)
                                                                                       tCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCa             >  2:107231/1‑101 (MQ=255)
                                                                                         ttATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCaaa           <  1:1589132/101‑1 (MQ=255)
                                                                                           aTCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACg         >  2:822776/1‑101 (MQ=255)
                                                                                           aTCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACg         >  2:938871/1‑101 (MQ=255)
                                                                                             ccGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACggg       <  2:784009/101‑1 (MQ=255)
                                                                                                  cTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACGGGGGCGa  >  1:509610/1‑101 (MQ=255)
                                                                                                  cTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACGGGGGCGa  >  1:556581/1‑101 (MQ=255)
                                                                                                  cTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACGGGGGCGa  >  1:1419762/1‑101 (MQ=255)
                                                                                                  |                                                                                                    
GGCAGATGATGTTGTCAAAGAGTATGCGTCGTTAATGTCATTTCGATGATACCGTGCGACCTGGTCGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGTTGCTCTCCAGCAGAGTTGGATAAGGCGTTTACGCCGCATCCGGCAAGATCACCGTTTAGGCGTCACATCCGTTGTCCCCTGCAAACGGGGGCGA  >  129/8864‑9062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑