Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6062,631,7720AC37.5% 106.0 / 15.2 56intergenic (‑267/‑141)rpoE/nadBRNA polymerase, sigma 24 (sigma E) factor/L‑aspartate oxidase
Reads supporting (aligned to +/- strand):  ref base A (32/3);  new base C (0/21);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 1.50e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ATCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTAA  >  REL606/2631698‑2631840
                                                                          |                                                                    
aTCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTccac                                                                     <  1:1339358/76‑1 (MQ=255)
  cTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTccacca                                                                   >  2:884184/1‑76 (MQ=255)
   tgtgTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCAccag                                                                  <  1:1966361/76‑1 (MQ=255)
         aaaaTCCCCATTTACCTCCCTGAAGAGTAACCCAACGGCCTTTTTATTCCCCCCCCTAACCCCCCCCCAGCCAGTa                                                            <  2:802403/75‑1 (MQ=255)
           aaTGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCATCCAGTAAc                                                          <  2:243712/76‑1 (MQ=255)
              gCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTtc                                                       >  1:1013836/1‑76 (MQ=255)
                ccATTTAACTGCCTGAAGAGTACCCCAACGGCCTTTTTATTTCACCCCCTAACCCCCCCCCAGCCAGTAACTtctc                                                     <  2:1296099/76‑1 (MQ=255)
                  aTTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCtt                                                   >  2:1126610/1‑76 (MQ=255)
                    ttAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCtttt                                                 >  1:104096/1‑76 (MQ=255)
                     tAACTGCCTGAAGAGTACCCCAACGGCCTTTTTATTTCACCACCTAATCCCCCCCCAGCCAGTAACTTCTCttttt                                                <  2:540754/76‑1 (MQ=255)
                      aaCTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTtc                                               >  1:488028/1‑76 (MQ=255)
                      aaCTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTtc                                               >  1:25669/1‑76 (MQ=255)
                      aaCTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTtc                                               >  1:1455097/1‑76 (MQ=255)
                       aCTGCCTGAAGAGTACCCCACCGGCCTTTTTATTCCCCCCCCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTtct                                              <  1:1014940/76‑1 (MQ=255)
                       aCTGCCTGAAGAGTACCCCAACGGCTTTTTTATTTCCCCCCCTAACCCTCCCCCAGCCAGTAACTTCTCTTTTtct                                              <  2:682469/76‑1 (MQ=255)
                        cTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTtctc                                             <  1:1257184/76‑1 (MQ=255)
                         tGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTcg                                            >  1:1207398/1‑76 (MQ=255)
                          gCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTcgc                                           >  1:1637086/1‑76 (MQ=255)
                          gCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTcgc                                           >  1:1311318/1‑76 (MQ=255)
                          gCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTcgc                                           >  1:1155789/1‑76 (MQ=255)
                                agagTACCCCAACGGCTTTTTTATTTCACCCCCTAATCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCt                                     <  1:1627823/76‑1 (MQ=255)
                                agagTAACCCAACGGCCTTTTTATTTCCCCCCCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCt                                     <  1:1309601/76‑1 (MQ=255)
                                agagTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCCCCAGCCAGTAACTTCTCTTTTTCTcg                                            <  1:1946258/69‑1 (MQ=255)
                                agagTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTcg                                            >  2:1946257/1‑69 (MQ=255)
                                 gagTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTg                                    >  1:1493943/1‑76 (MQ=255)
                                    tAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGt                                 >  2:1715129/1‑76 (MQ=255)
                                     accccAACGGCTTTTTTATTTCACCCCCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTc                                <  2:1552747/74‑1 (MQ=255)
                                      aCCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCa                               >  1:385463/1‑76 (MQ=255)
                                       cccAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAg                              >  2:1981397/1‑76 (MQ=255)
                                       cccAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAg                              >  2:984425/1‑76 (MQ=255)
                                        ccACCGGCCTTTTTATTCCCCCCCCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGc                             <  1:1582537/76‑1 (MQ=255)
                                          aaCGCCCTTTTTATTTCCCCACCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCgt                           <  1:1729925/76‑1 (MQ=255)
                                           aCGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCgtg                          >  1:421704/1‑76 (MQ=255)
                                            cGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCgtgt                         >  2:483287/1‑76 (MQ=255)
                                               ccTTTTTATTCCCCCACCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTa                      <  2:352073/76‑1 (MQ=255)
                                                cTTTTTATTTCACCCCCTAACCCTCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAg                     <  2:397522/76‑1 (MQ=255)
                                                 tttttATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGc                    >  2:1575270/1‑76 (MQ=255)
                                                  ttttATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGcc                   >  1:1622925/1‑76 (MQ=255)
                                                  ttttATTCCCCCACCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGcc                   <  1:717253/76‑1 (MQ=255)
                                                   tttATTTCCCCCCCTAATCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCa                  <  1:822070/76‑1 (MQ=255)
                                                   tttATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCa                  >  1:1059956/1‑76 (MQ=255)
                                                    ttATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCAc                 >  2:473761/1‑76 (MQ=255)
                                                    ttATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCAc                 >  2:515903/1‑76 (MQ=255)
                                                     tATTTCCCCCCCTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACt                <  1:1752208/76‑1 (MQ=255)
                                                      aTTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGTCACTg               >  2:1092121/1‑76 (MQ=255)
                                                        ttCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTa             >  1:1980605/1‑76 (MQ=255)
                                                         tccccaccTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTaa            <  2:1696254/73‑1 (MQ=255)
                                                         tCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTaa            >  2:770047/1‑76 (MQ=255)
                                                         tCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTaa            >  1:111254/1‑76 (MQ=255)
                                                          caccacCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAAc           >  2:1886020/1‑76 (MQ=255)
                                                           cccaccTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACa          <  1:65939/75‑1 (MQ=255)
                                                            cccccTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACaa         <  1:2001107/73‑1 (MQ=255)
                                                            ccaccTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACaa         >  2:912370/1‑76 (MQ=255)
                                                              cccTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAat       <  1:1881249/75‑1 (MQ=255)
                                                               ccTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAata      >  1:1669013/1‑76 (MQ=255)
                                                               ccTAACCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAata      <  2:257824/76‑1 (MQ=255)
                                                                 tAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATAtt    >  1:706188/1‑76 (MQ=255)
                                                                  aaTCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTa   >  2:1162511/1‑76 (MQ=255)
                                                                   aTCCCCCCCCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTaa  <  2:1711341/76‑1 (MQ=255)
                                                                          |                                                                    
ATCTGTGTAGAAATGCCCATTTAACTGCCTGAAGAGTAACCCAACGGCCTTTTTATTTCACCACCTAATCCTCCACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCCTGCGTCAGCGTGTTTAGCCACTGTAACAAATATTAA  >  REL606/2631698‑2631840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑