Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP00927369,9000AC54.2% 12.1 / 22.4 24V370G (GTG→GGG) thiPthiamine/thiamine pyrophosphate ABC transporter permease ThiP
Reads supporting (aligned to +/- strand):  ref base A (6/5);  new base C (0/13);  total (6/18)
Fisher's exact test for biased strand distribution p-value = 3.43e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.99e-02
Rejected as consensus: Frequency below/above cutoff threshold.

GGCCGATAGTGTTGTTGAGCAGTAAAAAGAAGCCGGTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATAC  >  NZ_CP009273/69811‑69982
                                                                                         |                                                                                  
ggCCGATAGTGTTGTTGAGCAGTAAAAAGAAGCCGGTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCa                                                                                    >  1:932294/1‑90 (MQ=255)
          gttgttGAGCAGTAAAAAGAAGCCGGTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGc                                                                          >  1:831169/1‑90 (MQ=255)
             gttgAGCAGAAAAAAGAAGCCGGTAGCCAGCACACCCCCCGGCAGGGCGAGGATCAACATGCCGCTCATCCCCAGCCCCTGACCCGCCAg                                                                       <  1:38086/90‑1 (MQ=255)
                               gCCGGTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCg                                                     >  2:255418/1‑90 (MQ=255)
                                ccGGTACCCACCACAACCCCCGGCATGGCGAGGATCAACATGCCGCTCACCCCCAGCCCCTGCCCCGCCAGCATTTTCTGCCGCGCCCGc                                                    <  1:333632/90‑1 (MQ=255)
                                   gTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGt                                                 >  2:441524/1‑90 (MQ=255)
                                     aGCCAGCACAACCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCCCCTGCCCCGCCAGCATTTTCTGCCGCGCCCGCAGTTc                                               <  2:417335/90‑1 (MQ=255)
                                           cacaACCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACt                                         <  2:308822/90‑1 (MQ=255)
                                           cacaACCCCCGGCATGGCGAGGACCAACATGCCCCCCATCCCCAGCCCCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACt                                         <  1:441524/90‑1 (MQ=255)
                                           cacaACCCCCGGCAGGGCGAGGATAAACATGCCGCTCATCCCCAGCCCCTGCCCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACt                                         <  1:154436/90‑1 (MQ=255)
                                           acagaTCCCGGGAATGGGGAGGATAAACATGCCGCTCATCTCCAGCCCCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACt                                         <  2:577289/86‑1 (MQ=255)
                                               acccccGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTc                                     <  2:179173/88‑1 (MQ=255)
                                               aTCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTc                                     >  2:360215/1‑90 (MQ=255)
                                                     ggCATGGCGAGGATAAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATagc                               <  2:932294/90‑1 (MQ=255)
                                                         tGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATagcctgt                           >  1:577289/1‑86 (MQ=255)
                                                            cGAGGATCAACACCCCGCTCACCTCCAGCCCCTGCCCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGcatca                        <  1:18737/90‑1 (MQ=255)
                                                                        tGCCGCTCATCCCCAGCCCCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTa            <  2:144762/90‑1 (MQ=255)
                                                                        tGCCGCTCACCCCCACCCCCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTa            <  2:544607/90‑1 (MQ=255)
                                                                           cGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGc         <  2:321589/90‑1 (MQ=255)
                                                                           cGCTCATCCCCAGCCCCTGCCCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGc         <  2:695824/90‑1 (MQ=255)
                                                                           cGCTCATCCCCAGCCCCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGc         <  2:831169/90‑1 (MQ=255)
                                                                           cGCTCACCCCCACCCCCTGCCCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGc         <  1:174072/90‑1 (MQ=255)
                                                                                  ctcCAGCCCCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATac  <  2:19908/90‑1 (MQ=255)
                                                                                       gCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATagcag                             <  2:404750/58‑1 (MQ=255)
                                                                                       gCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATagcag                             >  1:404750/1‑58 (MQ=255)
                                                                                         |                                                                                  
GGCCGATAGTGTTGTTGAGCAGTAAAAAGAAGCCGGTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATAC  >  NZ_CP009273/69811‑69982

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑