Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009135,1590GA43.2% 52.0 / 21.1 45intergenic (+139/‑75)thrC/yaaXL‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (21/4);  new base A (0/19);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 6.43e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAA  >  NC_000913/5009‑5308
                                                                                                                                                      |                                                                                                                                                      
aaTCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGgag                                                                                                                                                        <  2:544246/151‑1 (MQ=255)
   catcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGACCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAAt                                                                                                                                                     <  2:650992/151‑1 (MQ=255)
      caGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaa                                                                                                                                                   <  1:142669/150‑1 (MQ=255)
       aGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaaca                                                                                                                                                 <  2:797335/151‑1 (MQ=255)
        gTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaacaa                                                                                                                                                <  1:574821/151‑1 (MQ=255)
        gTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaaca                                                                                                                                                 >  2:601696/1‑150 (MQ=255)
                    cATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTtctc                                                                                                                                    >  2:461424/1‑150 (MQ=255)
                        aTCTAAATCAGGCCGGGTTTGTTTTTAGGCAGCCCGTTTTTTTTATGAAAAAATTAGGAAAAAAAATGACGGGAAAAAAGGAAAAATTCTAAAAAAATGCGTTAATTTAGAGATTAGGATGGCGGAAAAAAACAA‑CCGCCGTTCTCATCg                                                                                                                                <  2:645385/150‑1 (MQ=255)
                            cAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTa                                                                                                                            >  1:39180/1‑150 (MQ=255)
                             aaTCAGGCGGGGTTTTCTTTTATGCAGCCCGGCTTTTTTATAAAAAAATTAGGGAAAAAAAGGACAGGAAAAAAGGAAAAATTCAAAAAAAATGCGTTAATGAAGAAATAAGGATGGCGAAAAAAAACAA‑CCGCCGTTCTCATCGAGTa                                                                                                                            <  2:230437/149‑1 (MQ=255)
                             aaTCAGCCCTGTTTTTCTTTTATAAAGCCCGCCTTTTTTATAAAAAAATAAGGGAAAAAAGAAAAAGGAAAAAAAGAAAATTTCTAAAAAGATGCGGTAATTTAGAAATGAGTAGTGGGAAAAAAAACAA‑CCGCCGTTCTCATCGAg                                                                                                                              <  2:882260/147‑1 (MQ=255)
                                   gCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCgg                                                                                                                    >  1:864681/1‑151 (MQ=255)
                                    ccGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCgg                                                                                                                    >  1:90011/1‑150 (MQ=255)
                                      ggttttttttttATGCACCCGGGTTTTTTTATAAAAAAATTAGGGAAAAAAAGGAAAGGAAAAAAGGAAAATTTCTAAATAAATGCGTTAACTTAGAAATTAGGATGGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGa                                                                                                                   <  2:827331/141‑1 (MQ=255)
                                      gggTTTGCTTTTATGCGGCCCGGTTTTTTAAAGAAAAAATTAGGGAGAAAAATGACAGGAAAAAAGGAAAAATTCTAAATAAATGGGATAATTTAGAGATTAGGTTTGGGGAAAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCgg                                                                                                                    <  1:307982/148‑1 (MQ=255)
                                                      aGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc                                                                                                 >  1:868999/1‑151 (MQ=255)
                                                        ccgggtttttttATAAAGAAATTTGGAAGAAAAATGAAAGGGAAAAGGGAAAAATTCTAAAAAAAGGCGTTAATTTAGAGATTAGGATTGGGGAAAAAAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc                                                                                                 <  1:199879/143‑1 (MQ=255)
                                                        cccGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCACCGGATATCGACCCATAACGGGCa                                                                                                >  2:361372/1‑150 (MQ=255)
                                                         ccGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAATAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAAt                                                                                              >  2:541854/1‑151 (MQ=255)
                                                              ttttttATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATa                                                                                          >  1:64987/1‑150 (MQ=255)
                                                                ttttAGAAAGAAATTATTAAAAAAATGGACGGGAAAAAAGGAAAAATCCTCAAAAAATGGGGAAGCTTGGAAATTGGGTGGGCGAAAAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaa                                                                                        <  1:325003/150‑1 (MQ=255)
                                                                  ttATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAgg                                                                                     >  1:524055/1‑151 (MQ=255)
                                                                     tGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGt                                                                                  >  2:348646/1‑151 (MQ=255)
                                                                      gaagaaATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGt                                                                                  >  1:409254/1‑150 (MQ=255)
                                                                          aaaTTAGGGAAAAAAATGAAAGGAAAAAAGGAAAAATTCACAAAAAATGCGGTAATTTAGAGATTAGGTTTGGGAAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCt                                                                             <  2:303698/151‑1 (MQ=255)
                                                                           aaTTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtg                                                                            >  2:404991/1‑151 (MQ=255)
                                                                                 ggAAAAAAATGACAGGAAAAAAGGAAAATTTCTCAATAAATGCGTTAACTTAGATTTTAGGATTGCGGAAAATAACAT‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaa                                                                       <  2:478577/150‑1 (MQ=255)
                                                                                 ggAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAAAAAAGGCGGTAACTTAGAGATTAGGATGGCGGAAAAAAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGa                                                                         <  1:866396/148‑1 (MQ=255)
                                                                                    gaAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCTAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                      >  2:583384/1‑148 (MQ=255)
                                                                                      aaaaaaaCAGGAAAAAAGGGAAAATTCAAAAAAATTGAGGTAATTTA‑AGATTTGGTTGGGGGAAAAATACAATCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATg                                                                 <  2:797675/145‑1 (MQ=255)
                                                                                      aaaaTGACAGGAAAAAAGGAAAAATTCTAAAAAAATGCGGTAACTTAGAGATTAGGATTGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATg                                                                 <  1:601718/151‑1 (MQ=255)
                                                                                                  aaaaaGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGt                                                      >  1:189391/1‑150 (MQ=255)
                                                                                                  aaaaaGGAAAAATTCTCAATAAATGCGGTAACTAAGAAATTAGGATGGAGAAAAAAAACAC‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTa                                                          <  2:395635/146‑1 (MQ=255)
                                                                                                     aaggaaaattccaaaaTAAATGCGGTAACTAAGAGATTAGGATTGGGGAAAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTc                                                  <  1:196488/137‑1 (MQ=255)
                                                                                                     aaGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTc                                                  >  2:286848/1‑151 (MQ=255)
                                                                                                           aatttataaacaggtGCGTTACCATAGGGATTAGGATGGCGAAAAAAACCAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCAc                                              <  2:485853/135‑1 (MQ=255)
                                                                                                            aaTTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACttt                                           >  1:12617/1‑151 (MQ=255)
                                                                                                               tctcAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTccc                                        >  1:213742/1‑151 (MQ=255)
                                                                                                                  aaaTAAATGCGGTAATTTAGAGATAGGGATTGGGGAAAATAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTgg                                     <  1:261946/150‑1 (MQ=255)
                                                                                                                   aaTAAAGGGGGTAATTTAGAGATTAGGATGGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTgg                                     <  1:867518/150‑1 (MQ=255)
                                                                                                                       aacgCGGTAACTTAGAAATAAGGATTGCGGAAAAAAACAT‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGtt                                   <  1:129129/145‑1 (MQ=255)
                                                                                                                                aCTAAGAGATAAGGATGGCGGAAAAAAACAC‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTc                         <  1:574135/149‑1 (MQ=255)
                                                                                                                                  ttAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCAt                     >  2:351572/1‑151 (MQ=255)
                                                                                                                                  ttAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCAt                     >  2:241649/1‑151 (MQ=255)
                                                                                                                                      agaTTAGGATTGCGGATAATAACAA‑CCGCTGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgc                  <  2:542010/150‑1 (MQ=255)
                                                                                                                                                   ggAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCgg    >  1:470268/1‑151 (MQ=255)
                                                                                                                                                     agaATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGTTCGCTCCCATGGCAGCACAGGCTGCGGa   >  1:645268/1‑150 (MQ=255)
                                                                                                                                                      gaATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGaa  >  1:304038/1‑150 (MQ=255)
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AATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAA  >  NC_000913/5009‑5308

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑