Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi3,891,5060CG21.4% 56.6 / 11.8 29intergenic (+23/‑109)tnaB/mdtLtryptophan transporter of low affinity/multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (12/10);  new base G (5/1);  total (18/11)
Fisher's exact test for biased strand distribution p-value = 3.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AATCAGATGTTCACGGTCTGGGGCGGCAATCTTATTCCGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGC  >  NC_000913_3_pae_pgi/3891364‑3891643
                                                                                                                                              |                                                                                                                                         
aaTCAGATGTTCACGGTCTGGGGCGGCAATCTTATTCCGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTCAATCCTTCAAGAAGCCCAGCATTCGcatgc                                                                                                                                     >  2:170046/1‑145 (MQ=255)
     gATGTTCACGGTCTGGGGCGGCAATCTTATTCCGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGCACCCAGCCCTTAACTGGcttctt                                                                                                                                >  2:287950/1‑149 (MQ=255)
     gATGTTCACGGTCTGGGGCGGCAATCTTATTCCGGCGATTGTCATTCTCTTTGGGATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGcttcta                                                                                                                                <  2:363296/149‑2 (MQ=255)
                        ggcAATCTTATTCCGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACtt                                                                                                             <  1:283277/149‑1 (MQ=255)
                          cAATCTTATTCCGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTAt                                                                                                           >  1:70046/1‑149 (MQ=255)
                                     cGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCAc                                                                                                               <  1:335887/134‑1 (MQ=255)
                                     cGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCAc                                                                                                               >  2:335887/1‑134 (MQ=255)
                                     cGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGc                                                                                                <  2:418389/149‑1 (MQ=255)
                                                                       tttGTGCTGGTTAGGTAACGTCTTTTCCGTGTTCCCTAAATTTGGCTAAATCCTTCAAGAATCCTGCCATTCGCTCGCTTCTTGTCTCTCAGGTAATCACTTATGTGAATATGGCAACTCGCATGCTCCTCCTTCACCACGTATGCttt                                                              <  2:81440/149‑1 (MQ=255)
                                                                        ttGCGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTg                                                             <  1:290048/149‑1 (MQ=255)
                                                                             cTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGc                                                                                                                              <  1:209392/79‑1 (MQ=255)
                                                                             cTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGc                                                                                                                              >  2:209392/1‑79 (MQ=255)
                                                                                         cGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAg                                            >  2:69199/1‑149 (MQ=255)
                                                                                                    tgtTACCTAAATTTGGCTAAATCCATCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGc                                 >  1:412498/1‑149 (MQ=255)
                                                                                                      ttACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACCGGTGGGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTGGccc                               >  1:351038/1‑149 (MQ=255)
                                                                                                         ccTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACATTACTATCAGGACGCTTTAGCCCATg                            >  1:474486/1‑149 (MQ=255)
                                                                                                          cTAAATTTGGCTAAATGCTTCAAGAAGCCAGCTATTGGCGGGCTTCTTGCCTCTCGGGAAAGCAGTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCAACTTACTATCTGGAGGCGTTCACCCaggg                           >  2:163822/1‑146 (MQ=255)
                                                                                                          cTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGccaaatt                           >  1:14945/1‑144 (MQ=255)
                                                                                                                    ccaaaTCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCttttt                 <  1:307332/147‑1 (MQ=255)
                                                                                                                     tAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCttt                                                              <  2:15410/103‑1 (MQ=255)
                                                                                                                     tAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCttt                                                              >  1:15410/1‑103 (MQ=255)
                                                                                                                       aaTCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAGATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGAt              <  1:346701/149‑1 (MQ=255)
                                                                                                                             gcAAGAAGCCAGCGAATGGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAg        >  1:280826/2‑149 (MQ=255)
                                                                                                                               aagaagCCAGCGAATGGCTGGCTTCTTGCCTCTCAGGAAATCAGTTATGTCCAAATGGCAACTCGCCGGATCCTCCTTCACCACGTATGCTTTGCCTCACCTTACTATCAGGACGCTTTAGCCCGTGGCCCGCGTTTTGGTTTTTAGtt      >  2:185766/1‑149 (MQ=255)
                                                                                                                               aagaagCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCATGACGCTTTAGCCCATGTCCCGCTTTTTGTTTTGTAGtt      >  2:387776/1‑149 (MQ=255)
                                                                                                                                agaagCCAGCGAATGGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGa                                          <  1:33762/112‑1 (MQ=255)
                                                                                                                                agaagCCAGCGAATGGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGa                                          >  2:33762/1‑112 (MQ=255)
                                                                                                                                agaagCCAGCGAATGGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGttt     >  1:434762/1‑149 (MQ=255)
                                                                                                                                   agccagccATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTCGTTTTGc  >  1:138473/1‑149 (MQ=255)
                                                                                                                                              |                                                                                                                                         
AATCAGATGTTCACGGTCTGGGGCGGCAATCTTATTCCGGCGATTGTCATTCTCTTTGGTATAACCGTGATTTTGTGCTGGTTCGGCAACGTCTTTAACGTGTTACCTAAATTTGGCTAAATCCTTCAAGAAGCCAGCCATTCGCTGGCTTCTTGCCTCTCAGGAAATCACTTATGTCCAAATGGCAACTCGCCTGATCCTCCTTCACCACGTATGCTTTGCGTCACCTTACTATCAGGACGCTTTAGCCCATGTCCCGCTTTTTGATTTGTAGTTTTGC  >  NC_000913_3_pae_pgi/3891364‑3891643

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: ‑