Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*U000963,269,9560TC25.6% 68.0 / 28.7 47intergenic (+354/+260)yhaC/rnpBuncharacterized protein YhaC/RNase P catalytic RNA component
Reads supporting (aligned to +/- strand):  ref base T (12/20);  new base C (3/8);  total (19/28)
Fisher's exact test for biased strand distribution p-value = 7.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.46e-02
Rejected as consensus: Frequency below/above cutoff threshold.

CCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTC  >  U00096/3269815‑3270054
                                                                                                                                             |                                                                                                  
gcGGTATCAATAAATCGCACTCAACAATCAGAAACCCGCCGGATCGGTTTATTACGTACATCAGGTTAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAAcc                                                                                             <  2:1144506/148‑1 (MQ=17)
    cATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAAcc                                                                                             <  1:1144504/145‑1 (MQ=255)
    cATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGGCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACccgcc                                                                                         <  2:1144503/149‑1 (MQ=255)
    cATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGGCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACccgcc                                                                                         <  2:1144501/149‑1 (MQ=255)
     aTGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTGATCTTTCTGCCCCTACAAAAGTAAAAAAccgccg                                                                                        >  2:1557962/1‑149 (MQ=255)
     aTGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGAAAAAACccg                                                                                           >  1:1144509/1‑146 (MQ=255)
       gAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGaa                                                                                      <  2:1144505/149‑1 (MQ=255)
         aTAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGc                                                                                    <  1:1144507/149‑1 (MQ=255)
         aTAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGc                                                                                    <  1:1144508/149‑1 (MQ=255)
              gcgcACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGaaaaaa                                                                                               >  1:1144511/1‑133 (MQ=255)
                 cACTCAACAAGCTGAAACCCGCCGCATCGGGTTATTACGTAAATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCaaaaa                                                                                               <  2:1144514/130‑1 (MQ=14)
                  aCTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGAAAAAAc                                                                                              >  1:1144514/1‑130 (MQ=255)
                   cTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTAc                                                                          <  1:1144516/149‑1 (MQ=255)
                      aacaaTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTaaaa                                                                                                <  2:1144518/124‑1 (MQ=255)
                      aacaaTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTaaaa                                                                                                >  1:1144518/1‑124 (MQ=255)
                       acaaTCTGAAACCCGCCGGAACGGTTTATTACGAACATCACGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTaa                                                                      <  1:1144519/149‑1 (MQ=255)
                           tCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGAAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCa                                                                  >  1:1144549/1‑149 (MQ=255)
                             tGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAgg                                                                <  2:1144520/149‑1 (MQ=255)
                              gAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGt                                                               <  1:1144521/149‑1 (MQ=255)
                                aaCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGa                                                             <  2:1144522/149‑1 (MQ=255)
                                   ccgccgGACCGGGTTATTACGTACATCAGGTCAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGGTg                                                              <  2:1144524/145‑1 (MQ=11)
                                   ccgccgGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAAc                                                          <  2:1144525/149‑1 (MQ=255)
                                    cgccgGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGAAAAAACCCGCCGAAGCGGGGTTTTACGTAAGCCAGGTGAAGCt                                                         >  1:1144524/1‑149 (MQ=14)
                                      ccgGACCGGTTTATTACGTACAACAGGTCAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGGTGAAACTGa                                                       <  2:1144554/149‑1 (MQ=11)
                                       cgGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCaaaa                                                                                                >  2:1144553/1‑107 (MQ=255)
                                          aaCGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGa                                                   <  2:1144527/149‑1 (MQ=255)
                                          aaCGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCaaaaa                                                                                               >  1:1144526/1‑105 (MQ=255)
                                                  attaCGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAAc                                                                                              <  2:1144523/98‑1 (MQ=255)
                                                   ttaCGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGc                                                                                    <  1:1144553/107‑1 (MQ=25)
                                                    taCGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAg                                                                 <  1:1144550/125‑1 (MQ=17)
                                                    taCGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAg                                                                 >  2:1144550/1‑125 (MQ=17)
                                                    taCGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAg                                                                                     <  2:1144526/105‑1 (MQ=12)
                                                        tagctCACGTAACACTTTCCGATAAGCCGCTTGCTTTTGTCTCTCGTGTCGCGGAAAGTGTTTCCTATTTCTGCCCCTCCACAAGTACAAACCCGCCGCAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGctttctt                                     <  2:1144534/145‑1 (MQ=2)
                                                           aTCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTg                                  <  1:1144532/149‑1 (MQ=38)
                                                                                 gCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGAt                                                  >  2:1144557/1‑111 (MQ=35)
                                                                                     ctttctttTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCACCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAgg                                                                >  1:1144533/1‑93 (MQ=37)
                                                                                                                      tcatCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGt              >  1:1144563/1‑110 (MQ=17)
                                                                                                                      tcatCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGt              <  2:1144563/110‑1 (MQ=17)
                                                                                                                        atCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGtcattca        >  1:1144564/1‑114 (MQ=17)
                                                                                                                         tCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCg                                            >  1:1144604/1‑77 (MQ=39)
                                                                                                                          cTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTc                       >  2:1144566/1‑97 (MQ=18)
                                                                                                                           tttCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTgg                   >  1:1144565/1‑100 (MQ=18)
                                                                                                                            ttCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGct                                          <  1:1144535/76‑1 (MQ=39)
                                                                                                                             tCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTgg                   >  1:1144567/1‑98 (MQ=18)
                                                                                                                              cTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCg                                            >  1:1144613/1‑72 (MQ=255)
                                                                                                                                    cTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATa                                                 >  1:1144617/1‑61 (MQ=40)
                                                                                                                                            gTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGTCATTCATCtt    <  2:1144567/98‑1 (MQ=17)
                                                                                                                                            gTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGCGTCGTGGACAGTCATTCATCTTTc  <  2:1144565/100‑1 (MQ=17)
                                                                                                                                             |                                                                                                  
CCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTC  >  U00096/3269815‑3270054

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑