Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,598,4990GT54.5% 2.1 / 13.0 11G66C (GGT→TGT) lsrDautoinducer 2 ABC transporter permease LsrD
Reads supporting (aligned to +/- strand):  ref base G (1/4);  new base T (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCC  >  NZ_CP009273/1598413‑1598563
                                                                                      |                                                                
tCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTTGATATTTTTTTTGGtt                                                               >  2:95574/1‑90 (MQ=255)
        aGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGAGCGGTATTTTTTTTTGTTCGACCATc                                                       >  1:233094/1‑90 (MQ=255)
                     gcattggcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTTTTTTGTTTGACCATCGGCCCCTGCGccc                                          >  2:83791/1‑89 (MQ=255)
                      cattggcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCcat                                         <  1:280785/90‑1 (MQ=255)
                      cattggcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCcat                                         <  1:83791/90‑1 (MQ=255)
                               tgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTTTTTTGTTTGACCCTCGGCCCCTGCGCCCTTGCATTggg                                >  2:457409/1‑90 (MQ=255)
                               tgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATGGGGATTTCTTTTTGTTTGACCATCGGCCCCTCCGCCATTGCATTggg                                >  1:285144/1‑90 (MQ=255)
                                    cccTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTAc                           <  1:95574/90‑1 (MQ=255)
                                    cccTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTAc                           <  2:6997/90‑1 (MQ=255)
                                     ccTACCGCTAACGATGGTGATTGTCAGTGGCGGGAGCGATATTTTGTTTTGTTCGACCATCCGCCCCCCCGCCCTTTCATTGGGGGGACt                          >  1:351675/1‑90 (MQ=255)
                                                             cAGTGGCGGGATCGATATTTTGTTTTGTTCGACCATCGGCCTCTGCGCCCTTTCATTTGGGGGACTGTTTTAAAGGGGGGGGGCGATGcc  >  1:96270/1‑90 (MQ=255)
                                                                                      |                                                                
TCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCC  >  NZ_CP009273/1598413‑1598563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑