Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273341,9440TC57.4% 26.3 / 91.2 68G35G (GGA→GGG) yahNLysE family transporter
Reads supporting (aligned to +/- strand):  ref base T (13/16);  new base C (20/19);  total (33/35)
Fisher's exact test for biased strand distribution p-value = 6.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CATCGCCCAGCGCCACGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATCCATAAATAAG  >  NZ_CP009273/341856‑342031
                                                                                        |                                                                                       
cATCGCCCAGCGCCACGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTcc                                                                                       >  2:134919/1‑91 (MQ=255)
cATCGCCCAGCGCCACGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTcc                                                                                       >  1:85874/1‑91 (MQ=255)
  tCGCCCAGCGCCACGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCg                                                                                     >  2:584925/1‑91 (MQ=255)
     cccAGCGCCACGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGAt                                                                                  <  1:666071/91‑1 (MQ=255)
       cAGCGCCACGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTa                                                                                >  1:517023/1‑91 (MQ=255)
              aCGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAg                                                                         >  2:660252/1‑91 (MQ=255)
              aCGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAg                                                                         >  1:622061/1‑91 (MQ=255)
               cGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGt                                                                        <  1:134919/91‑1 (MQ=255)
               cGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGt                                                                        <  2:494747/91‑1 (MQ=255)
               cGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGt                                                                        <  1:18167/91‑1 (MQ=255)
               cGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGt                                                                        <  2:720425/91‑1 (MQ=255)
                   cAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATc                                                                    >  1:479271/1‑91 (MQ=255)
                   cAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATc                                                                    >  2:214249/1‑91 (MQ=255)
                   cAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATc                                                                    >  2:637031/1‑91 (MQ=255)
                       ccGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGa                                                                <  2:401555/91‑1 (MQ=255)
                         gtgcAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAAc                                                              <  2:752895/88‑1 (MQ=255)
                         ggTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAAc                                                              >  1:133780/1‑91 (MQ=255)
                         ggTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAAc                                                              <  1:15235/91‑1 (MQ=255)
                         ggTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAAc                                                              <  1:714121/91‑1 (MQ=255)
                          gTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACa                                                             <  1:836290/91‑1 (MQ=255)
                           tCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAg                                                            <  1:861942/91‑1 (MQ=255)
                               cACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCt                                                        >  2:530403/1‑91 (MQ=255)
                                   ccTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACgg                                                    <  2:151146/91‑1 (MQ=255)
                                   ccTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGCCCTACgg                                                    >  2:656476/1‑91 (MQ=255)
                                    cTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGt                                                   >  2:136291/1‑91 (MQ=255)
                                     tGCGCGTCGAGCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTc                                                  <  2:231983/91‑1 (MQ=255)
                                     tGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTc                                                  <  1:457932/91‑1 (MQ=255)
                                     tGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTc                                                  <  2:620325/91‑1 (MQ=255)
                                     tGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTc                                                  <  2:681872/91‑1 (MQ=255)
                                      gcgcGTCGACCGGGAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCa                                                 >  1:599743/1‑91 (MQ=255)
                                      gcgcGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCa                                                 >  2:215738/1‑91 (MQ=255)
                                             gACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAAc                                          <  2:622061/91‑1 (MQ=255)
                                             gACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAAc                                          >  1:306429/1‑91 (MQ=255)
                                                cGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGc                                       <  1:32956/91‑1 (MQ=255)
                                                  gAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCAt                                     <  1:215738/91‑1 (MQ=255)
                                                     gCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCa                                  <  2:821353/91‑1 (MQ=255)
                                                       cAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCaaa                                <  1:271846/91‑1 (MQ=255)
                                                       cAGGCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCaaa                                >  1:765840/1‑91 (MQ=255)
                                                         ggCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAgg                              <  1:161263/91‑1 (MQ=255)
                                                         ggCTGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAgg                              <  2:517023/91‑1 (MQ=255)
                                                            tGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATc                           <  1:305708/91‑1 (MQ=255)
                                                            tGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATc                           <  1:334953/91‑1 (MQ=255)
                                                            tGGTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATc                           <  2:37814/91‑1 (MQ=255)
                                                             ggTTTGTACTACCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATcc                          <  2:16344/91‑1 (MQ=255)
                                                              gTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCa                         >  2:317386/1‑91 (MQ=255)
                                                                 tGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAg                      <  1:770157/91‑1 (MQ=255)
                                                                       acCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAg                      >  2:782302/1‑85 (MQ=255)
                                                                       acCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAg                      <  1:782302/85‑1 (MQ=255)
                                                                       acCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGAttt                >  1:742352/1‑91 (MQ=255)
                                                                       acCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGAttt                >  1:486676/1‑91 (MQ=255)
                                                                       acCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGAttt                >  2:57366/1‑91 (MQ=255)
                                                                       acCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGAttt                >  2:314764/1‑91 (MQ=255)
                                                                       acCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGAttt                >  2:61035/1‑91 (MQ=255)
                                                                       acCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGAttt                >  2:61448/1‑91 (MQ=255)
                                                                       acCACAAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGAttt                >  2:807654/1‑91 (MQ=255)
                                                                        ccACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTc               <  1:243900/91‑1 (MQ=255)
                                                                         cacaAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCa              <  1:528915/91‑1 (MQ=255)
                                                                          acaAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCAt             >  1:641866/1‑91 (MQ=255)
                                                                          acaAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCAt             >  2:107887/1‑91 (MQ=255)
                                                                          acaAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCACGCAAAGGATCCATAGTGATTTCAt             >  1:181491/1‑91 (MQ=255)
                                                                           caAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATc            <  1:491726/91‑1 (MQ=255)
                                                                           caAAGAGATTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATc            <  2:306429/91‑1 (MQ=255)
                                                                            aaaGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATcc           >  1:799326/1‑91 (MQ=255)
                                                                             aaGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATCCa          <  2:148222/91‑1 (MQ=255)
                                                                                 gaTTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATCCataaa      >  2:79006/1‑91 (MQ=255)
                                                                                 gaTTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATCCataaa      >  2:668138/1‑91 (MQ=255)
                                                                                 gaTTGGCCCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATCCataaa      >  2:225270/1‑91 (MQ=255)
                                                                                     ggCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATCCATAAATAAg  <  1:317386/91‑1 (MQ=255)
                                                                                        |                                                                                       
CATCGCCCAGCGCCACGCCCAGCCCGGTCAGCACCCCTGCGCGTCGACCGGAAGCCAGGCTGGTTTGTACTACCACAAAGAGATTGGCTCCCGGATTAAAAAAAGTAATCACGAACAGTCCTACGGTCAGGTAAACGGCATGCAAAGGATCCATAGTGATTTCATCCATAAATAAG  >  NZ_CP009273/341856‑342031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑