Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,941,8920TA24.1% 36.0 / 12.3 30noncoding (85/1542 nt)rrsC16S ribosomal RNA of rrnC operon
Reads supporting (aligned to +/- strand):  ref base T (12/10);  new base A (7/0);  total (19/11)
Fisher's exact test for biased strand distribution p-value = 6.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.04e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGC  >  NC_000913/3941780‑3942040
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agattAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAAt                                                                                                                  <  1:315462/146‑1 (MQ=1)
                                tgcagagTTTTATCATGGCTAATATTGAACGCTGGCGGCAGGCCTAACACATGCAAGGCGAACTTTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAac                                                                                  <  2:145875/146‑1 (MQ=1)
                                                                                         tCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTc                         >  2:980567/1‑149 (MQ=32)
                                                                                         tCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTc                         >  1:1619082/1‑149 (MQ=32)
                                                                                          cGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATTCCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCg                        >  1:165860/1‑149 (MQ=17)
                                                                                           gAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCgg                       >  2:399936/1‑149 (MQ=32)
                                                                                            aaCGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCggg                      >  2:733054/1‑149 (MQ=32)
                                                                                            aaCGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAACAGGGGGACCTTCggg                      >  2:1459960/1‑149 (MQ=17)
                                                                                                gTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACTGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTTCTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGCCCTTCGGGCatc                  >  2:184752/1‑149 (MQ=255)
                                                                                                 tAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCctct                 >  1:1547100/1‑149 (MQ=32)
                                                                                                  tcagcgAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGCCCAAAGAGGGGGACCTTCGGGCCTCtt                >  1:901273/6‑149 (MQ=255)
                                                                                                  aaCAGGAAACAGCTTGGTGTTGCGCTGACGATTGGCGGACGGGTGAGTAATGTCTGGGAAACTGACTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCtt                <  2:1728428/149‑1 (MQ=255)
                                                                                                  aaCAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTACTGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACTGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCtt                <  1:381417/149‑1 (MQ=17)
                                                                                                  aaCAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCtt                <  2:424773/149‑1 (MQ=32)
                                                                                                   aCAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTg               >  1:382312/1‑149 (MQ=32)
                                                                                                    cAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGc              <  1:271526/149‑1 (MQ=32)
                                                                                                    agcgAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGc              >  1:288889/4‑149 (MQ=12)
                                                                                                     gcgAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             >  1:301848/3‑149 (MQ=12)
                                                                                                     gcgAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             >  2:1503480/3‑149 (MQ=12)
                                                                                                     aGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             >  2:1069881/1‑149 (MQ=32)
                                                                                                     aGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGcc             <  1:436389/149‑1 (MQ=32)
                                                                                                      cgAAACAGCAAGCTGTTTCGCTGCCTAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCa            >  2:1048618/2‑149 (MQ=255)
                                                                                                      cgAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCa            >  1:17011/2‑149 (MQ=17)
                                                                                                       gacccAGCTTGCTGTTGCGCTGACGAGGGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCAt           <  1:501693/145‑1 (MQ=12)
                                                                                                       gAAACAGCAAGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCAt           >  2:302865/1‑149 (MQ=17)
                                                                                                       caaccAGATTGCTGTTTCCCGGACGAGTGGCGGACGCGGGAGTAATGTCTGGGAAAATGCCTGATGTACGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCAt           <  2:219009/145‑1 (MQ=11)
                                                                                                        aaaCAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATc          >  2:1796755/1‑149 (MQ=32)
                                                                                                         aaCAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCa         >  1:1472133/1‑149 (MQ=32)
                                                                                                           cAGCTGGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGa       <  1:1190780/149‑1 (MQ=21)
                                                                                                              cTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGAtgt    <  2:23159/149‑1 (MQ=34)
                                                                                                                tGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGc  <  1:1069881/149‑1 (MQ=34)
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AGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGC  >  NC_000913/3941780‑3942040

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑