Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA3,439,5880GC29.7% 65.3 / 32.3 37intergenic (‑79/+28)yhdN/rplQDUF1992 family protein/50S ribosomal subunit protein L17
Reads supporting (aligned to +/- strand):  ref base G (14/12);  new base C (7/4);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 7.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TCAAACTCACCTTTCGCTTGCGCTTCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCACGGAAGCCACACTTCAGAATACGAGTGTAACCACCGG  >  NC_000913_3_pae_tpiA/3439445‑3439728
                                                                                                                                               |                                                                                                                                            
tCAAACTCACCTTTCGCTTGCGCTTCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCCcggcgg                                                                                                                                        >  2:181050/1‑150 (MQ=255)
  aaaCTCACCTTTCGCTTGCGCTTCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGt                                                                                                                                      >  1:94476/1‑150 (MQ=255)
      tCACCTTTCGCTTGCGCTTCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGttttt                                                                                                                                  >  1:4505/1‑150 (MQ=255)
              cGCTTGCGCTTCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTg                                                                                                                          <  1:109611/150‑1 (MQ=255)
                       ttCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCCCGGCGGGttttttt                                                                                                                                >  4:44610/1‑135 (MQ=255)
                       ttCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCCCGGCGGGttttttt                                                                                                                                <  3:44610/135‑1 (MQ=255)
                                atGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTgcag                                                                                                        >  2:172151/1‑150 (MQ=255)
                                   gcgcTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGcagcag                                                                                                     >  2:175602/1‑150 (MQ=255)
                                                    cAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGaa                                                                                    <  2:94476/150‑1 (MQ=255)
                                                     aaGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGAAAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAAc                                                                                   >  1:113233/1‑150 (MQ=255)
                                                       gTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGa                                                                                 >  2:3510/1‑150 (MQ=255)
                                                            cacaTAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCa                                                                                                                     >  1:177625/1‑109 (MQ=255)
                                                            cacaTAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCa                                                                                                                     <  2:177625/109‑1 (MQ=255)
                                                                tAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGc                                                                        <  2:113233/150‑1 (MQ=255)
                                                                       tCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTa                                                                                                                >  3:4826/1‑103 (MQ=255)
                                                                       tCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTa                                                                                                                <  4:4826/103‑1 (MQ=255)
                                                                          aGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTg                                                                                                                          >  2:169515/1‑90 (MQ=255)
                                                                          aGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTg                                                                                                                          <  1:169515/90‑1 (MQ=255)
                                                                                       aaaGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAAc                                                                                   <  4:76191/116‑1 (MQ=255)
                                                                                       aaaGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAAc                                                                                   >  3:76191/1‑116 (MQ=255)
                                                                                          gagTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTc                                              <  2:9376/150‑1 (MQ=255)
                                                                                          gagTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTc                                              <  1:175602/150‑1 (MQ=255)
                                                                                               cAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTg                                         <  1:3510/150‑1 (MQ=255)
                                                                                                aGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGttttt                                                                                                                                  <  1:4060/60‑1 (MQ=255)
                                                                                                aGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGttttt                                                                                                                                  >  2:4060/1‑60 (MQ=255)
                                                                                                 gCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCa                                       >  1:69125/1‑150 (MQ=255)
                                                                                                         aGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCCCGGCGGGttttt                                                                                                                                  >  1:143140/1‑51 (MQ=21)
                                                                                                         aGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCCCGGCGGGttttt                                                                                                                                  <  2:143140/51‑1 (MQ=21)
                                                                                                                              gTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGcc                                                            >  3:28863/1‑100 (MQ=255)
                                                                                                                              gTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGcc                                                            <  4:28863/100‑1 (MQ=255)
                                                                                                                                  aaaaaaaCCCGCCCCGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAg                                                              <  3:69227/94‑1 (MQ=255)
                                                                                                                                  aaaaaaaCCCGCCCCGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAg                                                              >  4:69227/1‑94 (MQ=255)
                                                                                                                                   aaaaaaCCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGGTCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCACGGAAGCCACACTTCAGAATACGAGTGTAaccac     >  1:184378/1‑150 (MQ=255)
                                                                                                                                   aaaaaaCCCGCCCCGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCACGGAAGCCACACTTCAGAATACGAGTGTAaccac     >  1:64629/1‑150 (MQ=255)
                                                                                                                                     aaaaCCCGCCCCGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCAc                                      >  2:102148/1‑115 (MQ=255)
                                                                                                                                     aaaaCCCGCCCCGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCAc                                      <  1:102148/115‑1 (MQ=255)
                                                                                                                                      aaaCCCGCCCCGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCACGGAAGCCACACTTCAGAATACGAGTGTAACCACCgg  >  1:84987/1‑150 (MQ=255)
                                                                                                                                               |                                                                                                                                            
TCAAACTCACCTTTCGCTTGCGCTTCTGCTATATGGCGCTCTGCCCACTGGTCAAGTAACCACATAAATACTCCAGGGGATGAACAAAAAGAGTACAGCTATTGTAGATAAGTGGGGATACTACGGGTATAAAAAAACCCGCCGGGGCGGGTTTTTTTACGTTGCTTCAGATTACTCTGCAGCAGCTTCTGCTTTCTCTGAACGATCAACCAGCTCGATGTAAGCCATCGGCGCGTTGTCGCCTGCACGGAAGCCACACTTCAGAATACGAGTGTAACCACCGG  >  NC_000913_3_pae_tpiA/3439445‑3439728

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑