Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_017635663,6020TG61.5% ‑4.8 / 10.7 13A284A (GCA→GCC) ECW_RS03175type VI secretion system tip protein VgrG
Reads supporting (aligned to +/- strand):  ref base T (1/4);  new base G (3/5);  total (4/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.28e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CATATCTCCGGCGAACGGCTTGTTCCGCGCGCCACTTCTGCGTTGTTTCGCCAGCCGTCCATCTGCCAGCGGGCAAAGTTCT  >  NC_017635/663564‑663645
                                      |                                           
cATATCCCCGGAGAACGGTTTGTTCCGCGCGCCACTTCGGCGTTGTTTCg                                  <  2:978772/50‑1 (MQ=11)
 atatCTCCGGCGAACGGCTTGTTCCGCGCGCCACTTCTGCGTTGTTTCGc                                 >  2:1896529/1‑50 (MQ=38)
  tatCTGCGGAGAACGGCTTGTTCCGCGCGCCACTTCGGCGTTGTTTCGcc                                <  1:1774182/50‑1 (MQ=11)
  tatCTCCGGAGAACGGCTTGTTCCGCGCGCCACTTCGGCGTTGTTTCGcc                                <  1:1007056/50‑1 (MQ=11)
   atCTCCGGAGAACGGCTTGTTCCGCGCGCCACTTCGGCGTTGTTTCGc                                 >  1:436783/1‑48 (MQ=11)
    tctcCGGCGAACGGCTTGTTCCGCGCGCCACTTCTGCGTTGTTTCGCCa                               <  1:1288606/49‑1 (MQ=38)
        cGGAGAACGGCTTGTTCCGCGCGCCACTTCGGCGTTGTTTCGCCAGcc                            <  1:1745162/48‑1 (MQ=11)
         ggCGACCGGTTTGTCCCGCGCGCCACTTCTGCGTTGTTTCGCCAGCCGTc                         <  2:1687144/50‑1 (MQ=14)
            gAACGGCTTGTCCCGCGCGCCACTTCGGCGTTGTTTCGCCAGCCGTCCAt                      <  2:1401529/50‑1 (MQ=14)
                               ccACTTCTGCGTTGTTTCGCCAGCCGTCCATCTGCCAGCGGGCAAAGTTc   <  2:1420809/50‑1 (MQ=255)
                                cACTTCTGCGTTGTTTCGCCAGCCGTCCATCTGCCAGCGGGCAAAGTTCt  <  2:133963/50‑1 (MQ=255)
                                cACTTCGGCGTTGTTTCGCCAGCCGTCCATCTGCCAGCGGGCAAAGTTCt  >  1:1179546/1‑50 (MQ=255)
                                cACTTCGGCGTTGTTTCGCCAGCCGTCCATCTGCCAGCGGGCAAAGTTCt  >  1:276578/1‑50 (MQ=255)
                                      |                                           
CATATCTCCGGCGAACGGCTTGTTCCGCGCGCCACTTCTGCGTTGTTTCGCCAGCCGTCCATCTGCCAGCGGGCAAAGTTCT  >  NC_017635/663564‑663645

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑