Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,561,9950AT56.2% 4.6 / 21.5 16V362V (GTT→GTA) digHglycoside hydrolase family 10 protein
Reads supporting (aligned to +/- strand):  ref base A (0/7);  new base T (9/0);  total (9/7)
Fisher's exact test for biased strand distribution p-value = 8.74e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.80e-04
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTTAAGATCGAGCTGCTTTTTCAGTTCCGGTACGCCGCCGTTAATCATCCAGTCTGGCTCTATCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTGGTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAACGCGCGGCACTCCGTGAG‑AACGGCCA‑GTAAATTTGGGGAGCAATGTAATCCAGCAATCCTTGTTCCACCCATCGACGGGTGTCAGCGTAGGAT  >  NZ_CP009273/1561869‑1562124
                                                                                                                              |                                                                                                                                     
gTTAAGATCGAGCTGCTTTTTCAGTTCCGGTACGCCGCCGTTAATCATCCAGTCTGGCTCTATCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTGGTCGGTTTAACGACATCCG‑cc                                                                                                                          <  2:293034/139‑1 (MQ=255)
          aGCTGCTTTTTCAGTTCCGGTACGCCGCCGTTAATCATCCAGTCTGGCTCTATCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGGCCTGGGCGGTTTTTAGAAATCCGCCCCC‑CCAtttt                                                                                                                >  2:94252/1‑139 (MQ=255)
                          ccGGTACGCCGCCGTTAATCATCCAGTCTGGCTCTATCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTGGTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAAc                                                                                                <  2:213331/138‑1 (MQ=255)
                                               tcCAGTCTGGCTCTATCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTTCTCGTCGGGTTTAAGACAACCC‑CCCC‑CCATTTTTCCCACACGTCATAAACCGCGGCACTCCGTGGG‑AACgg                                                                         >  2:57863/1‑139 (MQ=255)
                                                    tCTGGCTCTATCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGACCTGGTCGGTTTTAACACCTACA‑CCCC‑CCATTTTTGCAACAACTCATAACACGCGGCGCCACGAGGG‑AACGGCCac                                                                     >  2:391810/1‑137 (MQ=255)
                                                              tCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTTGGCGGTTTTACGACATCCG‑CCCC‑CCATTTTTTCAACACGTCATAAACCGCGGCACCCCCTGAG‑AACGGCCC‑GTAAAAATgggg                                                         >  1:355769/1‑139 (MQ=255)
                                                                  tGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTGGTCGGTTTTACGACATCCG‑CCCC‑CCCTTTTGCCAACACGTCATAAAGCGCGGCACTCCCTGAGAAACGCCCG‑AAAAATTTgggggc                                                       >  1:421089/1‑136 (MQ=255)
                                                                  tGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGGGCTGGGCGGGTTTACGACAACCG‑CCCA‑CCAATTTTCCAAAACGGCCTAAAGCGGGGCGCCCCCGGGG‑AACGGCCA‑AGAAAAATggggggg                                                      >  2:183337/1‑135 (MQ=255)
                                                                      ggTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTGGGCGGGTTTACGACATCCG‑CCCA‑CCCTTTTTCCAAAAACGCATAAAGCGCGGCACCCCCGGGG‑GACGGCCC‑GGAAATTTTGGGGGGAATg                                                  >  2:194176/1‑138 (MQ=255)
                                                                        ttCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGGCCCTGTCGGGTTTACGACAACCC‑CCCC‑CCCATTTTTCAACACCCCCTAACGCGCCGCACCCCGGGGG‑AAAGGCCACGGAAATTTGGGG‑GGAATGTa                                                >  2:305895/1‑138 (MQ=255)
                                                                          cACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTGGTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAACGCGCGGCACTCCGTGAG‑AACGGCCA‑GTAAATTTGGGGAGCAATGTAAt                                              <  2:112046/138‑1 (MQ=255)
                                                                          cACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGGCCTGGGTGGTTTTAAGACCTCCG‑CCCACCCATTTTGCC‑ACAAGTCCTAACCCGCGGCACTCCGGGAG‑AAAGGCCA‑GGAAATTTTGGGGGCAATGGAAtt                                             >  1:303483/1‑138 (MQ=255)
                                                                                    ataGAAGGCGATACCGATATACAGGCGGGTCCTGGTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAACGCGCGGCACTCCGTGAG‑AACGGCCA‑GTAAATTTGGGGAGCAATGTAATCCAGCAATcc                                    <  1:179837/138‑1 (MQ=255)
                                                                                                          aGGCGGGTCCTGGTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAACGCGCGGCACTCCGTGAG‑AACGGCCA‑GTAAATTTGGGGAGCAATGTAATCCAGCAATCCTTGTTCCACCCATCGACGGgtgt             <  1:305895/139‑1 (MQ=255)
                                                                                                                      gTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAACGCGCGGCACTCCGTGAG‑AACGGCCA‑GTAAATTTGGGGAGCAATGTAATCCAGCAATCCTTGTTCCACCCATCGACGGGTGTCAGCGTAGGAt  <  1:183337/138‑1 (MQ=255)
                                                                                                                      gTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAACGCGCGGCACTCCGTGAG‑AACGGCCA‑GTAAATTTGGGGAGCAATGTAATCCAGCAATCCTTGTTCCACCCATCGACGGGTGTCAGCGTAGGAt  <  2:303483/138‑1 (MQ=255)
                                                                                                                              |                                                                                                                                     
GTTAAGATCGAGCTGCTTTTTCAGTTCCGGTACGCCGCCGTTAATCATCCAGTCTGGCTCTATCTTTGAAGGTTCACCCACTTTATAGAAGGCGATACCGATATACAGGCGGGTCCTGGTCGGTTTAACGACATCCG‑CCCA‑CCATTTTGCCAACACGTCATAACGCGCGGCACTCCGTGAG‑AACGGCCA‑GTAAATTTGGGGAGCAATGTAATCCAGCAATCCTTGTTCCACCCATCGACGGGTGTCAGCGTAGGAT  >  NZ_CP009273/1561869‑1562124

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑