Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi3,941,8910TA20.0% 47.2 / 10.8 25noncoding (84/1542 nt)rrsC16S ribosomal RNA of rrnC operon
Reads supporting (aligned to +/- strand):  ref base T (8/12);  new base A (3/2);  total (11/14)
Fisher's exact test for biased strand distribution p-value = 6.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.87e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGC  >  NC_000913_3_pae_pgi/3941870‑3942040
                     |                                                                                                                                                     
cGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCgg                       <  2:406946/150‑1 (MQ=32)
cGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCgg                       >  2:312103/1‑150 (MQ=32)
 gAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCggg                      >  1:578402/1‑150 (MQ=32)
 gAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCggg                      >  3:900211/1‑150 (MQ=32)
        aaCAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTg               <  2:799769/150‑1 (MQ=32)
          catgAAACAGCTTACTGTTTCGCTGACGAGTGCCCTTCGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTGCTAGAAACTGTAGCTAATACCGCATCACGTCGCACGACCAAAGAGTGGGACATTCGGGCCTCTTGcc             >  4:490298/4‑150 (MQ=11)
          cAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCgg                       >  1:265044/1‑140 (MQ=33)
          cAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCgg                       <  2:265044/140‑1 (MQ=33)
          cAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             >  4:788609/1‑150 (MQ=32)
          cAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             <  2:254136/150‑1 (MQ=32)
           aGGAAACAGCTTGCTGATTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGACGGGGACCTTCGGGCCTCTTGCCa            <  2:591560/150‑1 (MQ=17)
            cgAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGAAATCTCTGGGAACCTGCCTGATGGAGGGGGATAACTACCGGAACCGGTAGCTCATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTCCGGGCCTCTTGCCAt           >  2:1046182/2‑150 (MQ=11)
             gAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             <  3:806618/147‑1 (MQ=12)
             gAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             >  4:806618/1‑147 (MQ=12)
              aaaCAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATc          <  1:593153/149‑1 (MQ=32)
              aaaCAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATc          >  2:593153/1‑149 (MQ=32)
              aaaCAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCa         <  1:1132850/150‑1 (MQ=33)
              aaaCAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGc              >  3:546632/1‑145 (MQ=12)
              aaaCAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGc              <  4:546632/145‑1 (MQ=12)
               aaCAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAg        >  2:1456525/1‑150 (MQ=33)
                aCAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGa       <  2:318385/150‑1 (MQ=35)
                 cAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGACACTGCAGTATGGAGGGGGATAACTACTGGAAACGGTAGCCAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGAt      <  1:106801/150‑1 (MQ=11)
                 cAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGAt      <  2:183608/150‑1 (MQ=35)
                   gCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGGCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGAtgt    <  4:500931/150‑1 (MQ=25)
                    cTTGCTGTGTCGCTGACGAGTGGCGGACGGGGGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGAtgtg   <  3:126021/150‑1 (MQ=25)
                     ttGCTGTTTCGCTGGCGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAGCTACTGGAAACGGCAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGc  <  1:1559837/150‑1 (MQ=255)
                     ttGCTGTTTCGCTGACGAGTGGCGGACGGGTGATTAATGTCTGGGAAACTGCCTGGTGGAGGGGGATAACTACGGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGc  >  2:893114/1‑150 (MQ=255)
                     ttGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTg               >  2:367730/1‑137 (MQ=33)
                     ttGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTg               <  1:367730/137‑1 (MQ=33)
                     |                                                                                                                                                     
CGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGC  >  NC_000913_3_pae_pgi/3941870‑3942040

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑