Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0129673,650,7670AG20.0% 281.2 / 20.0 135intergenic (+48/‑91)cspA/ysaERNA chaperone/antiterminator CspA/protein YsaE
Reads supporting (aligned to +/- strand):  ref base A (31/77);  new base G (27/0);  total (58/77)
Fisher's exact test for biased strand distribution p-value = 1.41e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

Only 100 of 139 total aligned reads displayed.

GCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCTATTATTATTTTTGTGAAGAA  >  NC_012967/3650696‑3650837
                                                                       |                                                                      
gCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGa                                                                        <  1:4985962/72‑1 (MQ=255)
gCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGa                                                                        <  1:3973894/72‑1 (MQ=255)
  tGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGAtt                                                                      <  1:4056558/72‑1 (MQ=255)
  tGGTAACGTAACCAGCCTGTAATCTCTGATTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGAtt                                                                      <  1:8717/72‑1 (MQ=255)
   gttaacgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGAGGAttt                                                                     <  2:1410080/70‑1 (MQ=255)
    gtaacgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGAtttt                                                                    <  1:4715353/72‑1 (MQ=255)
    ataacgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGAtttt                                                                    <  2:3315672/71‑1 (MQ=255)
     taacgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAG‑ATCTAAGATCCCTGCCATTTGGCGGGGAtttttt                                                                  <  2:9085830/72‑1 (MQ=255)
      aacgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCAGCCATTTGGCGGGGAtttttt                                                                  >  2:577956/1‑72 (MQ=255)
       acgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGAttttttt                                                                 >  1:660041/1‑72 (MQ=255)
        cgtaacCAGCCTGTAATCTCTGCTTAAGAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTa                                                                <  2:7693973/72‑1 (MQ=255)
        cgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTa                                                                <  2:1867975/72‑1 (MQ=255)
        cgtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTa                                                                <  1:6839325/72‑1 (MQ=255)
         gtaacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTAt                                                               <  1:4760087/72‑1 (MQ=255)
          taacCAGCCTGTAATCTCTGCTTAAAAGCNCAGAATCTAAGATCCCTGCCATTTGGCGGGGGtttttttttt                                                              >  2:490126/1‑72 (MQ=255)
          taacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGTCGGGGATTTTTTTAtt                                                              >  1:8417628/1‑72 (MQ=255)
          aacccAGCCTGTATTCTCTGCTAAAAAGCACAAAATCTAAGACCCCTGCCATTTGGGGGGGATTTTTTTAtt                                                              <  2:3690491/69‑1 (MQ=255)
           aacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTAttt                                                             >  2:8597432/1‑72 (MQ=255)
           aacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTAttt                                                             <  1:551427/72‑1 (MQ=255)
           aacCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTAttt                                                             <  2:6125128/72‑1 (MQ=255)
            acCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTg                                                            >  1:3009899/1‑72 (MQ=255)
            acCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTNATTTg                                                            >  2:439638/1‑72 (MQ=255)
             ccAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGt                                                           <  1:2258720/72‑1 (MQ=255)
              cAGCGTGTAATCTCTGCTAAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGtt                                                          <  2:1009426/72‑1 (MQ=255)
              cAGCCTGTAATCTCTGCTTAAAGGCACAGAATCTAAGACCCCTGCCTTTTGGCGGGGATTTTTTTATTTGtt                                                          <  2:716346/72‑1 (MQ=255)
              cAGCCTGTAATCTCTGCTNAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGtt                                                          <  1:3767398/72‑1 (MQ=255)
                gCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCTATTTGGCGGGGATTTTTTTATTTGtttt                                                        <  1:2765108/72‑1 (MQ=255)
                gCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGtttt                                                        <  1:9501551/72‑1 (MQ=255)
                gCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGtttt                                                        <  2:6759494/72‑1 (MQ=255)
                gCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGtttt                                                        <  1:8596359/72‑1 (MQ=255)
                 ccTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTc                                                       <  1:7389758/72‑1 (MQ=255)
                 ccTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTc                                                       <  1:9028321/72‑1 (MQ=255)
                  cTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGttttta                                                      >  2:5279937/1‑70 (MQ=255)
                  cTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCa                                                      <  2:3983544/72‑1 (MQ=255)
                   tGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGttttttg                                                     >  2:3548549/1‑69 (MQ=255)
                   tGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAg                                                     <  1:7829649/72‑1 (MQ=255)
                   tGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAg                                                     <  2:4331664/72‑1 (MQ=255)
                    gTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAgg                                                    <  1:2683782/72‑1 (MQ=255)
                    gTAATCTCTGCTAAAAACNACAGAATCTAAGACCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAgg                                                    <  1:3788330/72‑1 (MQ=255)
                     tAATCTCTTCTTAAAAGAACAAAATCTAAATACCCTACCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGa                                                   <  1:2217207/72‑1 (MQ=255)
                     tAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGa                                                   <  1:6007255/72‑1 (MQ=255)
                     tAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGa                                                   >  1:8092737/1‑72 (MQ=255)
                     tAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGa                                                   <  1:5966149/72‑1 (MQ=255)
                     tAATCTCTACTTAAAAGCACAGAATCTAAGATCCCTGCCATTCGGCGGGGATTTTTTTATTTGTTTTCAGGa                                                   <  2:7620776/72‑1 (MQ=255)
                      aacctctGCTAAAAAGCACAGAATCTAAGATCCCTGCCATTGGGCGGGGATTTTTTTATTTGTTTTCAGGaa                                                  <  2:6470447/69‑1 (MQ=255)
                      aaTCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGGaa                                                  >  2:8911264/1‑72 (MQ=255)
                      aaTCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaa                                                  >  2:3038817/1‑72 (MQ=255)
                      aaTCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaa                                                  <  2:5932385/72‑1 (MQ=255)
                      aaTCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaa                                                  <  2:9746941/72‑1 (MQ=255)
                      aaTCTCGCCTAAAAAGCACAAAACCAAAAACCCCTCCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaa                                                  <  1:8603592/72‑1 (MQ=255)
                       aTCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaaa                                                 <  1:5029488/72‑1 (MQ=255)
                        tctcTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGGTTTTTTATTTTTTTTTTGGaaat                                                >  1:1614429/1‑72 (MQ=255)
                         ctctGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGGaaata                                               >  2:3162131/1‑72 (MQ=255)
                         ctctGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaaata                                               >  2:2572872/1‑72 (MQ=255)
                          tctGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaaataa                                              <  2:4352266/72‑1 (MQ=255)
                          tctGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGCATTTTTTTATTTGTTTTCAGGgaataa                                              >  1:5718458/1‑72 (MQ=255)
                           ctGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTTTTTGTTTTCAGGaaataaa                                             >  2:6729739/1‑72 (MQ=255)
                           ctGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaaataaa                                             >  2:2053651/1‑72 (MQ=255)
                            tGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaaataaat                                            <  2:9339204/72‑1 (MQ=255)
                            tGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaaataaat                                            <  1:3520883/72‑1 (MQ=255)
                             gCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTTTTTGTTTTTAGGGaattaata                                           >  1:8942355/1‑72 (MQ=255)
                              cTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAataaataa                                          <  2:204859/72‑1 (MQ=255)
                              cTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAataaataa                                          <  2:5515157/72‑1 (MQ=255)
                                tAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGCAAATAAATAatc                                        >  1:2388309/1‑72 (MQ=255)
                                tAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAatc                                        <  1:1495089/72‑1 (MQ=255)
                                 aaaaGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGGAAATAAATAatcg                                       >  2:1521193/1‑72 (MQ=255)
                                  aaaGCACAGAATCTGAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAatcga                                      <  2:4876976/72‑1 (MQ=255)
                                  aaaGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAatcga                                      <  1:9783805/72‑1 (MQ=255)
                                  aaaGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAatcga                                      <  2:4287250/72‑1 (MQ=255)
                                  aaaGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAatcga                                      <  1:7462088/72‑1 (MQ=255)
                                    aGCACAGAATCTAAGACCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAatcgatc                                    <  1:1461197/72‑1 (MQ=255)
                                      cacaGAATCTAAGATCCCTGCCATTTGGCGGGGGGTTTTTTTTTTTTTTTCAAGGAAAAAATAATACATcgc                                  >  2:1397042/1‑72 (MQ=255)
                                      cacaGAATCTAAGACCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATcgc                                  <  1:6309701/72‑1 (MQ=255)
                                       acaGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGGAAATAAATAATCGATcgcg                                 >  1:4683199/1‑72 (MQ=255)
                                       acaGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATcgcg                                 <  2:8630027/72‑1 (MQ=255)
                                        caGAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGt                                >  1:8463522/1‑72 (MQ=255)
                                        caGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTTAGGAAATAAATAATCGATCGCGt                                >  2:1804090/1‑72 (MQ=255)
                                         aaaaTCTAAGATCCCGGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGta                               <  1:2319399/70‑1 (MQ=255)
                                         aGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGta                               >  2:9200548/1‑72 (MQ=255)
                                          gAATCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGtaa                              >  2:5986712/1‑72 (MQ=255)
                                          gAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGtaa                              <  1:9033524/72‑1 (MQ=255)
                                           aaTCTAAGTCCCCTGCCATTTGGGGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGtaat                             <  2:1723512/72‑1 (MQ=255)
                                           aaTCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGtaat                             <  1:9761971/72‑1 (MQ=255)
                                           aaTCTAAGACCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGtaat                             <  2:6224156/72‑1 (MQ=255)
                                           aaTCAAAGACCCCTGCAATTGGGGGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGtaat                             <  2:8637512/72‑1 (MQ=255)
                                             tCTAAGATCCCTGCCATTTGGCGGGGGTTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGGGtaaaaa                           >  2:5191476/1‑72 (MQ=255)
                                             tCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGtaataa                           <  1:9224096/72‑1 (MQ=255)
                                                aaGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAAt                        <  2:4662255/72‑1 (MQ=255)
                                                  gATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCt                      <  2:4728627/72‑1 (MQ=255)
                                                  gATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCt                      >  2:4195040/1‑72 (MQ=255)
                                                  gATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCt                      >  2:9410673/1‑72 (MQ=255)
                                                   aTCCCTGCCATTTGGCGGGGGTTTTTTTAATTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATNta                     >  2:813734/1‑72 (MQ=255)
                                                     cccTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCtatt                   >  1:7629851/1‑72 (MQ=255)
                                                             tttGGCGGGGGTTTTTTTATTTTTTTTTAGGAAATAAATAATCGATCGCGTAATAAAATCTATTATTAtttt           >  2:1145516/1‑72 (MQ=255)
                                                              ttGGCGGGGGTTTTTTTTTTTGTTTTCAGGGAATAAATAATCGATCGCGTAATAAAATCTATTATTAttttt          >  1:6593741/1‑72 (MQ=255)
                                                              ttGGCGGGGGTTTTTTTATTTGTTTTCAGGAAATAAATAATAGATCGCGTAATAAAATCTATTATTAttttt          >  2:644554/1‑72 (MQ=255)
                                                                   ggggATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCTATTATTATTTTTGTgaa     >  1:9237695/1‑72 (MQ=255)
                                                                   ggggATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCTATTATTATTTTTGTgaa     >  2:2509603/1‑72 (MQ=255)
                                                                    gggATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCTATTATTATTTTTGTgaag    <  1:2961603/72‑1 (MQ=255)
                                                                      gATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCTATTATTATTTTTGTgaagaa  >  2:9463154/1‑72 (MQ=255)
                                                                       |                                                                      
GCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAATAAATAATCGATCGCGTAATAAAATCTATTATTATTTTTGTGAAGAA  >  NC_012967/3650696‑3650837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑