Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273726,2060AC57.1% 10.2 / 12.0 14T390P (ACC→CCC) rhsCrhs element protein RhsC
Reads supporting (aligned to +/- strand):  ref base A (4/2);  new base C (0/8);  total (4/10)
Fisher's exact test for biased strand distribution p-value = 1.50e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.20e-02
Rejected as consensus: Frequency below/above cutoff threshold.

CAGCTAAACCCGGCAGGCTTAAGTTACACGTATCAGTATGAGAAGGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGGGTGGTGAAAAAGGAACA  >  NZ_CP009273/726146‑726282
                                                            |                                                                            
cAGCTAACCCCGGCGGGCTTAAGTTCCCCGTATCAGTATGAGAAGCCCCCCCCCCCCATCCCCGACCGCCTGAACCGCCGTGAAGTCCTg                                                 <  2:457282/90‑1 (MQ=9)
       cccgggCAGGTTAAAGTTACACGTATCAGTAGGAGAAGGCCCCCACCCCCACCCCCGAAACCCTAAACCGCCGTGAAGTCCTGCACACGc                                          <  1:590095/86‑1 (MQ=9)
       ccccGGCAGGCTTAAGTTACACGTATCAGTATGAGAAGGCCCCCATCACCATCCCCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGc                                          <  1:3936/89‑1 (MQ=14)
       ccccGCCAGCCTTAAGTCACACGTATAGGTAGGAGAAGGCCCCCACCCCCACCACCGACACCCTGAACCGCCGTGAAGTCCTGCACACGc                                          <  2:550944/89‑1 (MQ=255)
                        tACACGTATCAGTATGAGAAGGCCCGCATCCCCATCCCCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTg                         <  1:437420/90‑1 (MQ=17)
                                 gaGTAGGAGAAGGCCCGCCCCCCCACCCCCGACCGCCGGACCCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGggtg                <  2:474474/89‑1 (MQ=17)
                                 cattATGAGAAGGCCCCACCCACCCCCCCCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGggtg                <  2:501703/87‑1 (MQ=17)
                                        agaAGGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGGGTGGTGaaaa         >  1:100037/1‑90 (MQ=255)
                                        agaAGGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGGGTGGTGaaaa         >  1:232015/1‑90 (MQ=255)
                                         aaaGGCCCCCACCCCCACCCCCGACGGCCTAAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGGGTGGTGaaaaa        <  2:232015/89‑1 (MQ=17)
                                             gACCGCATCACCATCACCGACAGCCTGAACCGCCGTGa                                                        <  1:314194/38‑1 (MQ=40)
                                             gACCGCATCACCATCACCGACAGCCTGAACCGCCGTGa                                                        >  2:314194/1‑38 (MQ=255)
                                             gACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGGGTGGTGAAAAAGGaa    >  1:544169/1‑90 (MQ=255)
                                               ccGCACCCCCATCCCCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGGGTGGTGAAAAAGGAaca  <  1:102403/90‑1 (MQ=14)
                                                            |                                                                            
CAGCTAAACCCGGCAGGCTTAAGTTACACGTATCAGTATGAGAAGGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTCCTGCACACGCAGGGTGAAGGCGGGCTGAAGCGGGTGGTGAAAAAGGAACA  >  NZ_CP009273/726146‑726282

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑