Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0020941,702,5680TG44.4% 51.1 / 20.9 63intergenic (‑247/+8)rpsA/mnmA30S ribosomal protein S1/tRNA‑specific 2‑thiouridylase MnmA
Reads supporting (aligned to +/- strand):  ref base T (21/14);  new base G (28/0);  total (49/14)
Fisher's exact test for biased strand distribution p-value = 9.82e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ATTTTCTTTTGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCCATCATAGAAAACAACGGC  >  CP002094/1702475‑1702665
                                                                                             |                                                                                                 
aTTTTCTTTTGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTa                                                                                              >  2:1364205/1‑99 (MQ=255)
   ttCTTTTGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTAttt                                                                                           >  2:322481/1‑99 (MQ=255)
     cTTTTGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTAttttt                                                                                         >  1:715503/1‑98 (MQ=255)
      ttttGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTAtttttt                                                                                        >  2:1211453/1‑97 (MQ=255)
      ttttGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTAt                                                                                        >  2:271655/1‑99 (MQ=255)
      ttttGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTAt                                                                                        >  2:565398/1‑99 (MQ=255)
       tttGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATAGGCAGGTTCGGATTTTAtt                                                                                       >  1:1096476/1‑99 (MQ=255)
        ttGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTg                                                                                      >  2:576657/1‑99 (MQ=255)
             aaCATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTTTTGAtttt                                                                                 >  1:849353/1‑99 (MQ=255)
             aaCATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTTATAtt                                                                                 >  2:460787/1‑99 (MQ=255)
              aCATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTTTTGATATTg                                                                                >  2:595429/1‑99 (MQ=255)
              aCATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATATTg                                                                                >  2:1448273/1‑99 (MQ=255)
                aTTTTCTTTTTTATTAATTTTAAAGTAATAAATAGCAACTTTATATGAAAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCa                                                                              <  2:768553/99‑1 (MQ=255)
                    tCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTTTTAATTTTTTAATCTTTAATCAc                                                                          >  2:600110/1‑99 (MQ=255)
                     cTTTTTTAATAATCTTAAAGTAATAAAGAACTAATTTATATGAAAAAAAAAACCTGCCATTTTATTGGCAGTTTCGTATTTTATTGATATTGCATCACt                                                                         <  2:1266799/99‑1 (MQ=255)
                        ttttATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACtttt                                                                      <  2:406354/99‑1 (MQ=255)
                         tttATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACttttt                                                                     >  2:1489234/1‑99 (MQ=255)
                          ttattaATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTg                                                                    >  2:454263/1‑99 (MQ=255)
                            attaATCTTAAATAAATAAATAGAATCTTTATATAATAAAAAAACCCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGtt                                                                  <  1:1264589/99‑1 (MQ=255)
                             ttaATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTc                                                                 >  1:145409/1‑99 (MQ=255)
                             ttaATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTc                                                                 >  2:614028/1‑99 (MQ=255)
                              taATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAACCCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCt                                                                <  2:245373/99‑1 (MQ=255)
                               aaTCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTTTTTATATTTCATCACTTTTTTTTCtt                                                               >  1:708064/1‑99 (MQ=255)
                                aTCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATATTGCATCACTTTTTGTTCttt                                                              >  2:606758/1‑99 (MQ=255)
                                aTCTTAAAGTAATAAATACCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGCATTTTTTTGATATTGCATCACTTTTTGTTCttt                                                              >  2:1465032/1‑99 (MQ=255)
                                 tCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTTCATCACTTTTTGTTTTTTg                                                             >  2:1399125/1‑99 (MQ=255)
                                 tCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTTTTTATATTGCATCACTTTTTGttttttt                                                             >  1:940608/1‑98 (MQ=255)
                                 tCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTTTTATTGCATCACTTTTTGTTATTTg                                                             >  2:1317112/1‑99 (MQ=255)
                                 tCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTg                                                             >  2:432533/1‑99 (MQ=255)
                                  cTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATATTGCATCACTTTTTGTTCttttt                                                            >  2:141274/1‑97 (MQ=255)
                                    tAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGGATTTTATTGATATTGCATCACTTTTTGTTTTTTGTaa                                                          >  2:1617231/1‑99 (MQ=255)
                                     aaaGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTTTTTTTAAg                                                         >  2:787394/1‑99 (MQ=255)
                                     aaaGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAg                                                         <  2:1570442/99‑1 (MQ=255)
                                      aaGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTTGGATTTTATTGATATTGCATCCCTTTTTGTTCTTTTTAAGc                                                        >  2:1191176/1‑99 (MQ=255)
                                      aaGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTTTTTATATTGCATCACTTTTTGTTTTTTGTAAGc                                                        >  1:1145588/1‑99 (MQ=255)
                                      aaGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTTATATTGCATCACTTTTTGTTCTTTTTAAGc                                                        >  2:1630556/1‑99 (MQ=255)
                                           ataaataGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTTTTTTTATTTCATCACTTTTTTTTTTTTTTAAGCTACGt                                                   >  1:779674/1‑99 (MQ=255)
                                              aataGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCaa                                                <  2:882304/99‑1 (MQ=255)
                                                taGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTTTTTATATTTCATCACTTTTTTTTCTTTTTAAACTACGTCAATc                                              >  2:1267182/1‑99 (MQ=255)
                                                      cTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTTGTGTTTTTTTTTTATTTCATTACTTTTTTTTTTTTTTTAACTACGTCAATCATTTCt                                        >  1:1048748/1‑99 (MQ=255)
                                                      cTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGGATTTTATTGATATTGCATCACTTTTTTTTCTTTTTAAGCTACGTCAATCATTTCt                                        >  1:436028/1‑99 (MQ=255)
                                                       tttATATGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTTTTGATATTTCATCACTTTTTTTTTTTTTTAAGCTACGTCAATCATTGCTc                                       >  2:884323/1‑99 (MQ=255)
                                                       tttATATGAAAAAAAAACCCTGCCATTTTATTGGCAGGTTCGTATCTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTc                                       <  1:1095454/99‑1 (MQ=255)
                                                           tatGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATATTTCATCACTTTTTGTTCTTTTTAAGCTACGTCAATCATTTCTccacc                                   >  2:26963/1‑99 (MQ=255)
                                                            atGATAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTTTTTATATTGCATCACTTTTTGTTCTTTTTTAGCTACGTCAATCATTGCTccacca                                  >  1:1085985/1‑99 (MQ=255)
                                                             tGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCaa                                 <  2:1576729/99‑1 (MQ=255)
                                                             tGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCaa                                 <  1:1269143/99‑1 (MQ=255)
                                                              gaaaaaaaaacCCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAg                                <  1:271655/96‑1 (MQ=255)
                                                              gATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTTTTTATATTTCATCACTTTTTGTTCTTTTTAAGCTACGTCAATCATTGCTCCACCAAg                                >  1:32614/1‑99 (MQ=255)
                                                                tAAAAAAAACCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTTTAAGCTACGTCAATCATTTCTCCACCAAGGc                              >  2:1451798/1‑99 (MQ=255)
                                                                  aaaaaaaCCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCAt                            <  1:1516307/99‑1 (MQ=255)
                                                                    aaaaaCCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCAttc                          <  2:88071/99‑1 (MQ=255)
                                                                      aaaCCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATAATACATCACTTTTTGTTCTTTTTAAACTACGACAACAAATTCTCCACCAAAGCcttctt                        >  2:335319/1‑99 (MQ=255)
                                                                       aaCCTGCCATTTTATTGGCAGGGTCGTATTTTATTGATATTGCCTCACTTTTTGTTTTTTGTAAGATACGGCAATACTTGCTTCCCCAAGGGAttcttc                       >  1:1362345/1‑99 (MQ=255)
                                                                           tGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCca                   >  2:793956/1‑99 (MQ=255)
                                                                              cATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCcatca                >  2:1658832/1‑99 (MQ=255)
                                                                              cATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCcatca                <  1:1654489/99‑1 (MQ=255)
                                                                              cATTTTATTGGCAGGGTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCcatca                >  2:179993/1‑99 (MQ=255)
                                                                                ttttATTGGCAGGGTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCCATCATa              >  2:585436/1‑99 (MQ=255)
                                                                                   tATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTTTAAGCTACGTCAATCATTGCTCCACCAAGGCCTTTTTCTCCATCATAGaa           >  2:1410078/1‑99 (MQ=255)
                                                                                           ggTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCCATCATAGAAAACAACgg   >  2:531561/1‑99 (MQ=255)
                                                                                            gTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCCATCATAGAAAACAACGGc  >  1:537740/1‑99 (MQ=255)
                                                                                            gTTCGGATTTTATTGATATTCCATCACTTTTAGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCCATCATAGAAAACAACGGc  >  2:1153255/1‑99 (MQ=255)
                                                                                             |                                                                                                 
ATTTTCTTTTGAAAACATTTTCTTTTTTATTAATCTTAAAGTAATAAATAGCAACTTTATATGATAAAAAAAACCTGCCATTTTATTGGCAGGTTCGTATTTTATTGATATTGCATCACTTTTTGTTCTTTGTAAGCTACGTCAATCATTGCTCCACCAAGGCATTCTTCTCCATCATAGAAAACAACGGC  >  CP002094/1702475‑1702665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑