Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_hsa_pgi4,037,2270GT23.7% 52.0 / 13.8 38intergenic (+10/‑33)ileT/alaTtRNA‑Ile/tRNA‑Ala
Reads supporting (aligned to +/- strand):  ref base G (18/11);  new base T (0/9);  total (18/20)
Fisher's exact test for biased strand distribution p-value = 1.33e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.43e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAGAAGCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTA  >  NC_000913_3_hsa_pgi/4037078‑4037373
                                                                                                                                                     |                                                                                                                                                  
aagaagCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACg                                                                                                                                                    <  2:92868/150‑1 (MQ=34)
aagaagCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACg                                                                                                                                                    >  2:3248718/1‑150 (MQ=34)
  gaagCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGc                                                                                                                                                  >  1:741434/1‑150 (MQ=34)
  gaagCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGc                                                                                                                                                  <  1:4622/150‑1 (MQ=34)
  gaagCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTAAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGTTTCAAGTCCACTCATGACTACCAAATTTGCACgga                                                                                                                                                  >  2:730173/1‑149 (MQ=255)
  gaagCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTATACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGc                                                                                                                                                  >  2:2599846/1‑150 (MQ=21)
     gCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCata                                                                                                                                               >  2:778601/1‑148 (MQ=21)
      ccttCTTTGAAGTGCTCACACAGATTGTCTGATGAAAAAGACCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTCGTTAGAGCGCACCCCTGATAAGGATGAGGTCGTTGGTTCAAGTCCACTCAGGCCTAACAAATTTTCACGGCAAAt                                                                                                                                              >  1:1310329/3‑150 (MQ=11)
      cGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGCGCGCACACCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAAt                                                                                                                                              >  1:2769372/1‑150 (MQ=21)
      cGTTCTTTGAAGTGCTCACACAGATTGGCTGATGAAAATGAGCAGTAAAACCTCTACCGGCGTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAAt                                                                                                                                              <  2:3405451/150‑1 (MQ=255)
       gTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAAtt                                                                                                                                             >  2:859181/1‑150 (MQ=34)
       gTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAAtt                                                                                                                                             >  2:3205969/1‑150 (MQ=34)
       gTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAAtt                                                                                                                                             >  2:1909142/1‑150 (MQ=34)
       gTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAAtt                                                                                                                                             <  2:147770/150‑1 (MQ=34)
       gTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTATACAGGCTTGTAGCGAAGGTGGTTTGAGCGCACCCCTGATAAGGGTGAGGTCGGTTGTTCAAGTCCACTCAGGCCAACAAAATTTGCACGGCAAAtt                                                                                                                                             >  1:766032/1‑150 (MQ=11)
        ttCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAATCCTCTACAGGCTTGTAGCGCAGGTGGTTATAGCGCTCCCCTGATAAGGGTGAGGGCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAAttt                                                                                                                                            <  2:2794630/150‑1 (MQ=11)
         tCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTg                                                                                                                                           <  1:3062436/150‑1 (MQ=32)
         tCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTg                                                                                                                                           >  1:1817906/1‑150 (MQ=32)
         tCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTGGTAGCTCAGGTGGTTATAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTg                                                                                                                                           <  2:2599178/150‑1 (MQ=11)
         gcTTTGAAGTGCTCACACAGAATGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCATGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTg                                                                                                                                           <  1:764917/149‑1 (MQ=17)
          cTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGa                                                                                                                                          <  2:2250962/150‑1 (MQ=32)
          cTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGa                                                                                                                                          >  2:4078683/1‑150 (MQ=32)
          cTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGGGAGGGCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGa                                                                                                                                          <  1:30637/150‑1 (MQ=17)
          cTTTGAAGTGCTCACACAGATTGTCTGAGGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGAGAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTgg                                                                                                                                          <  2:1722773/150‑2 (MQ=11)
          cTTTGAAGTGCTCACACAGATTGTCTGAAGAAAATGAGCAGTAAAACCTCTACACGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGGCGGTGGTGCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGa                                                                                                                                          <  1:160695/150‑1 (MQ=255)
          cTTTGAAGTGCGCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTgg                                                                                                                                          <  1:2198638/150‑2 (MQ=255)
           tttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTggt                                                                                                                                         <  2:3346736/150‑3 (MQ=12)
           tttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTggt                                                                                                                                         <  1:3898458/150‑3 (MQ=12)
           tttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGaa                                                                                                                                         >  1:366970/1‑150 (MQ=32)
           tttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGGGGTTAGAGCGCACCCCTGATAAGGGTGAGGGCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGaa                                                                                                                                         <  2:2808066/150‑1 (MQ=17)
           tttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGT‑AAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTggta                                                                                                                                        <  1:1905363/150‑4 (MQ=11)
            ttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACCGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTggta                                                                                                                                        <  1:1130671/150‑4 (MQ=11)
            ttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGTCTTGTAGCTCAGGTGGTTAGAGAGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCCGTGCAAATTTggta                                                                                                                                        <  2:2822805/150‑4 (MQ=11)
            ttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAag                                                                                                                                        >  2:314242/1‑150 (MQ=32)
            ttGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAag                                                                                                                                        >  2:1563247/1‑150 (MQ=32)
            atGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGAAAAACCTCTACAGGCTTGAAGCTCAGGGGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAag                                                                                                                                        <  2:3651326/149‑1 (MQ=12)
             tGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAaga                                                                                                                                       >  2:3014307/1‑150 (MQ=32)
             tGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAaga                                                                                                                                       >  1:2983030/1‑150 (MQ=32)
             tGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAaga                                                                                                                                       >  1:143477/1‑150 (MQ=32)
                                                                                                                                   ggacTACCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATaaaaa                 >  1:3699653/4‑150 (MQ=1)
                                                                                                                                           aattttGCACGGCAAATTTGAAGTGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCa         <  2:2188994/147‑1 (MQ=1)
                                                                                                                                                  caaggCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTa  >  2:2544247/4‑150 (MQ=1)
                                                                                                                                                     |                                                                                                                                                  
AAGAAGCGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAATGAGCAGTAAAACCTCTACAGGCTTGTAGCTCAGGTGGTTAGAGCGCACCCCTGATAAGGGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCTACCAAATTTGCACGGCAAATTTGAAGAGGTTTTAACTACATGTTATGGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTA  >  NC_000913_3_hsa_pgi/4037078‑4037373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑