Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24403,440,3630AC52.4% 12.2 / 21.2 21A24A (GCA→GCC) CJ019_03266hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (3/7);  new base C (11/0);  total (14/7)
Fisher's exact test for biased strand distribution p-value = 1.03e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.90e-03
Rejected as consensus: Frequency below/above cutoff threshold.

TAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGC  >  KT2440/3440235‑3440490
                                                                                                                                |                                                                                                                               
tAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCCCTGGCGGCGCCCGGGCCGCCggg                                                                                                                           >  3:98336/1‑135 (MQ=255)
 aGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCGGGCGGCGCCCCGGCCGCCgggg                                                                                                                          >  2:274011/1‑135 (MQ=255)
  gCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCggggg                                                                                                                         >  7:79460/1‑134 (MQ=255)
        gTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCCGCCTGGGTGTGGcc                                                                                                                   >  8:61879/1‑134 (MQ=255)
         gcgggacgaCCGCAAGGCCCTCTCCACGCGAGCGCTCGAGGGGCTGCAGGGAGCGCGTGGGCCACCCGCCGGGGCGCCGTGGCGCGGCTGCGGGCCGCCCGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAg                                                                                                                  <  7:244908/132‑1 (MQ=255)
           tGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCCCCCGCGCTGGCGCCGCCCGGGCCCCCCGGCTGTGGCCGGc                                                                                                                >  4:47697/1‑135 (MQ=255)
                      aaGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCCGGCGGCGCCCGGGCCGCCGGGGGGTTGGCGGCCACCGCCta                                                                                                       >  5:231674/1‑133 (MQ=255)
                      aaGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCAGGCCGCGCCCGGGCCGCCGGGGTGTGGCAGGCCAACGCCta                                                                                                       >  3:117987/1‑133 (MQ=255)
                           ccTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCCGCCGGGGGGTGGCCGGCCCACCCCGATAAGgcg                                                                                                >  2:288630/1‑135 (MQ=255)
                             tctACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCCCTGGCGGCGCCCGGGCAGCCTGGGTGTGGGAGGCCACCGCCGATAAGGCGCa                                                                                              >  3:362924/1‑135 (MQ=255)
                                aCAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCAGCCGGGGGGTGGGAGGCCCCCCCCGATAAGGcgccgcg                                                                                           >  6:132064/1‑134 (MQ=255)
                                            tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCGGGGGGCGCCCGGGCCGCCGGGGGGTTGGAGGCCCACCCCGATAATGCGCCGCTCGCGGATCACGc                                                                               >  2:222480/1‑135 (MQ=255)
                                                        aGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCCGCCCGGGGGGGGGCGGCCCCCCCCGAAAAGGCGCCGCGCGCCGCTCAGGCCGCGGACTTCgg                                                                   >  4:301582/1‑135 (MQ=255)
                                                             gcgcGTGGGCCCCCCGGCGGGGGGGGGGGGCGCTGCGGCGGGCCGCCCGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCCGGCCGATGACTTCGGCAAGc                                                              <  3:304743/135‑1 (MQ=255)
                                                               gcTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGGCGCCCGCGCGGGCGGCGCCCGGGCCGCCGGGGGGTGGGCGGCCCCCGCCGAGAAGGCGCAGCGCGCGGCTCAGGCCGCGGACTTCGGCGAGCAg                                                            >  4:141635/1‑135 (MQ=255)
                                                               gcTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCTGGGGGCGGCCGGGGCGCCGGGGGGGGGGCGGGCCACCCCGATTATGCGCAGCGCGCGGGTCAGGGCGAGGACGTCGGcgcgcac                                                            >  6:6115/1‑129 (MQ=255)
                                                                                   ggCCGGGGCGCGGCTCCTGCCCGCCCGCGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgcgc                                        <  7:267358/134‑1 (MQ=255)
                                                                                                  gcgggCCGCCCGGGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCg                         <  4:98336/132‑1 (MQ=255)
                                                                                                        cgccCGCGCGGCCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGaa                   <  1:288630/135‑1 (MQ=255)
                                                                                                                cgggcggcGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGAGCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgcag           <  7:61879/133‑1 (MQ=255)
                                                                                                                         cccGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAgcgc  <  6:226587/135‑1 (MQ=255)
                                                                                                                                |                                                                                                                               
TAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGC  >  KT2440/3440235‑3440490

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: ‑