Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24401,313,9430AC51.7% ‑0.6 / 15.2 31L614R (CTG→CGG) CJ019_01235hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (10/4);  new base C (2/13);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 2.51e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.99e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ACGGGATGAAGGTGTCCGGCGCCAGCAACCCTTCCTGTGGATGCCGCCAGCGCACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTACAGGGCGATGTCGGCGCAGCGGAT  >  KT2440/1313809‑1314073
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aCGGGATGAAGGTGTCCGGCGCCAGCAACCCTTCCTGTGGATGCCGCCAGCGCACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCa                                                                                                                                    >  5:250766/1‑135 (MQ=255)
   ggATGATGGTGTCCGGCGCCAGAAACCCTTGGTGTGGAGGCCGCCAGCTCACCAAGGCGGCGCCCGGGAGGTTTCGGTGGTGGTCCTGGGGGTTGGGGGGGTGTTAATGCAACTCGAACTCCTCTTTGGGCTgg                                                                                                                                  <  4:144916/134‑1 (MQ=255)
                 ggCGCCAGCAACCCTTCCTGTGGATGCCGCCAGCGCACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCg                                                                                                                   >  3:181614/1‑135 (MQ=255)
                 ggCGCCAGCAACCCTTCCTGTGGATGCCGCCAGCGCACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGGCg                                                                                                                   >  7:300715/1‑135 (MQ=255)
                 ggCGCCAGCAACCCTTCCTGTGGATGCCGCCAGCGCACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCGGCGCAGGTCg                                                                                                                   >  3:175260/1‑135 (MQ=255)
                      cAGCAACCCTTCCTGTGGATGCCGCCAGCGCACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCCGGGCCCTGCGCAGGTCGTtctc                                                                                                              >  7:233760/1‑135 (MQ=255)
                             cgttCCTGGGGAGGCCGCCAGCGCACCAAGGCCGCGACCGCGACGATTCGCAGGGCGTCCCGGCGGTCGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCGTTCTCCAGCTgg                                                                                                       <  8:290540/133‑1 (MQ=255)
                                         tGCCGCCCGCGCACCAAGGCCTCGCCCGCGACTATGCGCTGGTCGTCCCGGCGGTCGGGTGGCTGTTAATGCAACGCGACCGCCTCATTGCCCAGGGCCGTGGGCAGGTCGTTCTCCAGCTGGCGGCGGTACTgg                                                                                           <  6:280870/135‑1 (MQ=255)
                                          gccgccAGCGCACCAAGGCCTCGACCGCGCCGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGGCGTTCTCCCGCTGGCGGCGGTACTGGa                                                                                          >  3:33809/1‑135 (MQ=255)
                                               ctgcccACCATGGCGTCGACCGCGAGTAGGCGCTGGGCGTCCCGGCGGACGCGGGGCTGGTAATCCACCTCGAGCTCCTCATTGCGCAGGGCCCGGCGCAGGTCGTTCTCCTGCTGGCGGCGGTACTGGATctgc                                                                                     <  8:345982/130‑1 (MQ=255)
                                                  cgcACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTgg                                                                                  >  3:247224/1‑135 (MQ=255)
                                                  cgcACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCGTTCGACGGGTGGCGGCGGTTCTGGATCGGGTgg                                                                                  >  5:316258/1‑135 (MQ=255)
                                                    cACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCCGGGCCCGGCGCAGGTCGGTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGt                                                                                 >  7:44664/1‑134 (MQ=255)
                                                    cACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCGGCGCAGGTCGGTCTCCAGCTGGCGGCGGTACTGGATCtggtgggt                                                                                >  7:296366/1‑133 (MQ=255)
                                                                 aCCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAAc                                                                    >  1:259343/1‑134 (MQ=255)
                                                                  ccGCGACTCTTCGCCGGGCGGCCCGGCGGTAGCGGGGCGGGAAACGCCACGCGACCTCCTCATCGCGCAGGGCCCTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGa                                                                  <  3:54906/135‑1 (MQ=255)
                                                                    gcgACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCCGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTGATTTCGGCAACGaa                                                                 >  6:232099/1‑134 (MQ=255)
                                                                     ccccgaTTCGCCGGGGGGCCCGGGGGTCGGGGGGCTGTTAATGAACCTCAAACTCCTCATTGCGCCGGCCCGTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGt                                                               <  2:323912/132‑1 (MQ=255)
                                                                                 gggcgtcCCGGGGGTTGGGTGGCTGTAAACCCAACACGACCTCCTCATTCCGCCGGCCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATgtgt                                                   <  1:350487/132‑1 (MQ=255)
                                                                                       ccAGGCGGTAGCGGGGCTGGAAAGCCAACTCGAACTCCTCATTGCGCCGGGCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTc                                             <  2:249626/135‑1 (MQ=255)
                                                                                             ggTAGCGGGGCTGGTAAGGCACCTCCAACTCCTCATTGCGCGGGGCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCgg                                       <  2:19020/135‑1 (MQ=255)
                                                                                             ggTAGCGGGGCTGGTAAGGCAACTGTCACTCCTTATTCCGCCGGGCCGTCCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTTGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCgg                                       <  4:207641/135‑1 (MQ=255)
                                                                                                  gggggCTGGTAACGCAACTCCAACTCCTCTTTGCGCCGGGCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTg                                  <  3:102383/132‑1 (MQ=255)
                                                                                                  gggggCTGGAAACGCACCCCCACCTCCCCCTCGCGCCGGCCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTg                                  <  3:55024/132‑1 (MQ=255)
                                                                                                  gggggCGGGAAATCCAACTCCCACACCTCATTGCGCCGGCCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTg                                  <  8:44664/132‑1 (MQ=255)
                                                                                                  ggTGGCTGTTAATGCAACACGACCGCATAATAGCCCCGGGCCCTCCGCAGTTCGGTCTCCAGCTGGCGGCTGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGACATGTGTTCTTTCCATCGGCCtt                                   <  4:254192/133‑1 (MQ=255)
                                                                                                           tAATCCAACGCCAACTCCTCATGGCGCCGGGCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTa                          <  7:30311/134‑1 (MQ=255)
                                                                                                                   cTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTACAGGGCGAt                 >  8:306090/1‑135 (MQ=255)
                                                                                                                          gcctcATGCCGCCGCGCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTACAGGGCTATGTCGgcg          <  5:271761/134‑1 (MQ=255)
                                                                                                                             tcATGGCCCCGGGCCGTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTACAGGGCGATGTCGGCGCAg       <  2:66707/135‑1 (MQ=255)
                                                                                                                               aTTGCGCCGGGCCCTGCCCAGGTCGTTCTCCAGCTGGCGGAGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTACAGGGCGATGTCGGCGCAGCg     <  1:245945/135‑1 (MQ=255)
                                                                                                                                   cgcCGGGCCCGGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTACAGGGCGATGTCGGCGCAGCGGAt  <  3:204195/134‑1 (MQ=255)
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ACGGGATGAAGGTGTCCGGCGCCAGCAACCCTTCCTGTGGATGCCGCCAGCGCACCAAGGCCTCGACCGCGACGATTCGCAGGTCGTCCAGGCGGTAGCGTGGCTGGTAATGCAACTCGAACTCCTCATTGCGCAGGGCCCTGCGCAGGTCGTTCTCCAGCTGGCGGCGGTACTGGATCTGCTGGTTCATTTCGGCAACGAAGTAGCGCCATGTGTTCTTTCCATCGGCCTTGGCCTGGTACAGGGCGATGTCGGCGCAGCGGAT  >  KT2440/1313809‑1314073

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑