Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,523,5550AC53.8% 5.7 / 12.7 13pseudogene (1397/2037 nt)BW25113_RS07645RHS repeat protein
Reads supporting (aligned to +/- strand):  ref base A (3/3);  new base C (0/7);  total (3/10)
Fisher's exact test for biased strand distribution p-value = 6.99e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.13e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTAC  >  NZ_CP009273/1523468‑1523613
                                                                                       |                                                          
tGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCAcc                                                          <  2:420545/90‑1 (MQ=255)
      tcatcaGCGAAGACGGCAATACGGCGGGGCGGGGGGAGTATGATGAAGGGGGCACCCAGCTTAATGAGGAGACCCCGCATCCCCTGcccc                                                    <  1:235340/90‑1 (MQ=17)
                               gTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagca                           >  2:383275/1‑90 (MQ=255)
                                         gAGTATGAGGAATGGGGCACCCAGCTAAAGGAGGAGAACCCGCATCCCCTGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag                 <  1:399910/90‑1 (MQ=17)
                                              tgatgaATGGGGCACCCAGCTTAATGAGGAGACCCCGCATCCCCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTc            <  2:375947/90‑1 (MQ=17)
                                              tgatgaAGGGGGCAACCAGCTTAAGGGGGAGACCCCGCATCCCCTGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTc            <  1:267968/90‑1 (MQ=17)
                                                   aaTGGGGCAACCAGCTTAATGAGGAGAACCCGCATCCCCTGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGc       <  1:158879/90‑1 (MQ=255)
                                                   aaTGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTc            <  1:166304/85‑1 (MQ=255)
                                                   aaTGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTc            >  2:166304/1‑85 (MQ=255)
                                                    aTGGGGAACCCAGCTAAATGGGGAGACCCCGCATCCCCGGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCt      <  1:714/90‑1 (MQ=17)
                                                    aTGGGGAAACCAGCTTAATGAGGAGAACCCGCATCACCTGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCt      <  1:145000/90‑1 (MQ=255)
                                                     tGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTg     >  1:117462/1‑90 (MQ=255)
                                                        ggCAACCAGCTTAATGAGGAGAACCCGCATCCCCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTAc  <  2:117462/90‑1 (MQ=255)
                                                                                       |                                                          
TGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTAC  >  NZ_CP009273/1523468‑1523613

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑