Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,549,5660TC53.8% 3.5 / 13.2 13S215G (AGT→GGT) rtcARNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base T (5/1);  new base C (0/7);  total (5/8)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
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.

ACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCC  >  NZ_CP009273/3549502‑3549652
                                                                |                                                                                      
caggTATTCCCCGGCCCCGGGTCGCGCGGCAGGTTATGAATTTTCTGTTCATGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGc                                                               <  2:29826/88‑1 (MQ=255)
  gttATTCCCCGCCCCCTGGCCGCGGGGCGGTTTATGAATTTTCTTTTCAGGAAGGAAAAACCTCCCCGCCAGTGTAGCGATTTCACGCTc                                                             <  1:18662/88‑1 (MQ=255)
          ccGCCCCCTGGCCGCGCGGCGGTTTATAAATTTTCTTTTAAGGCGGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAt                                                     <  1:123677/90‑1 (MQ=255)
             gCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAtctg                                                  >  1:29826/1‑87 (MQ=255)
                      cgcgggGCGGTTTATAAATTTTCTTTTCAGGAAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCacac                                         <  1:114470/90‑1 (MQ=255)
                      cgcgcgGGGGTTTAGAAATTTTCTGTCCATGCGGGAAAACCCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCacac                                         <  1:90895/90‑1 (MQ=255)
                                tttATGAATTTTTTGTCCCTGAAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAg                               <  2:213691/89‑1 (MQ=255)
                                      aaTATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTtc                         >  1:186854/1‑90 (MQ=255)
                                         atTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTcc                      >  1:213691/1‑90 (MQ=255)
                                          ttCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa                     >  1:79157/1‑90 (MQ=255)
                                           tCTGTTCAGGCGGGAAAAACCCCCCCGCCAGTGTATCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc                    <  2:7199/90‑1 (MQ=255)
                                                   ggCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACCCCAGCTAATAGAACTTCCCCACGCATCTGc            <  1:307671/89‑1 (MQ=255)
                                                             aaCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTcc  >  1:75527/1‑90 (MQ=255)
                                                                |                                                                                      
ACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCC  >  NZ_CP009273/3549502‑3549652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑