Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009135,1590GA41.5% 47.6 / 13.5 41intergenic (+139/‑75)thrC/yaaXL‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (21/3);  new base A (0/17);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 7.52e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGA  >  NC_000913/5025‑5307
                                                                                                                                        |                                                                                                                                                     
tATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGtt                                                                                                                                      >  2:451132/1‑151 (MQ=255)
     aTTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCAt                                                                                                                                 >  1:625585/1‑151 (MQ=255)
            cAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTa                                                                                                                           >  2:160713/1‑150 (MQ=255)
             caTCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAAt                                                                                                                         >  1:233523/2‑151 (MQ=255)
                  ggCGGGTTTTGTTTTTATGCAGCCCGGTTTTTTTATAAAAAAATTATGGAAAAAAAGGAAAGGAAAAAGGGAGAAATTCTAAAAAAA‑GGGGTTAACTTAGAGATTAGG‑ATGGGGGAAAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCg                                                                                                                    <  2:501438/151‑1 (MQ=255)
                  ggCGGGTTTTGTTTTTATGCAGCCCGGTTTTTTTATAAAAAAATTAGGAAAAAAAAGGACAGGAAAAAAGGAAAAATTCTAAAAAAA‑TGCGGTAACTTAGAGATTAGG‑ATGGGGGAAAAAAACA‑ACCGCCGTTCTCATCGAGTAAtct                                                                                                                       <  2:68294/148‑1 (MQ=255)
                      ggttttGTTTTTAGGCAGCCCGGTTTTTTTAAAAAAAAATTAGGAAAAAAAATGACAGGAAAAAAGGAGAATTTCTCAATAAG‑TGCGGTAACTTAGATATTAGG‑ATTGGGGAAAATAACA‑CCCGCCGTTCTCATCGAGTAAtct                                                                                                                       <  2:229368/141‑1 (MQ=255)
                      ggttttGCTTTTATGAAGCCGGGTTTTTTTAAAAAAAAATTATGAAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGata                                                                                                                <  1:395743/148‑1 (MQ=255)
                          ttGTTTTTATGCAGCCCGGTTTTTATAGAAAAAAATTATGGAAAAAAATGACAGGAAAAAAGGAAAAATTCTCAATAAC‑TGCGTAATCTTAGAGTTAAGG‑TTGGAGGAAAATACCA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATc                                                                                                              <  1:241787/149‑1 (MQ=255)
                                  aggccgCCCGGTTTTTTTATAAAAAATTTAGGGAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAAAAAA‑GGCGGTAACTAAGAGATTAGG‑ATGGGGGAAAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAAc                                                                                                    <  2:197270/146‑1 (MQ=255)
                                        cccGGGTGTTTTATGAAGAAATTAGGGAAAAAAAGGAAGAGAAAAAAGGAAAAATTCTAAAAAAA‑GGCGTAAACTTGGAATTAAGG‑TTTGGGGAAAATACCA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCAt                                                                                                       <  1:330615/142‑1 (MQ=255)
                                        cccGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCa                                                                                               >  2:562672/1‑150 (MQ=255)
                                           ggtttttttAGAAAAAAATTAGAAAAAAAAAGGACGGGAAAAAAGAAAAAATTCCAAATAAG‑TGCGGTAACTGAGTG‑TTAGGTTTTGGGGAAAATACAA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCa                                                                                               <  1:78309/144‑1 (MQ=255)
                                             tttttttAAAAAAAAATTATGAAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAAAAAA‑TGCGGTAATTTAGAGATTGGG‑ATTGGGGAAAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGAt                                                                                          <  2:377212/149‑1 (MQ=255)
                                             ttttttaATGAAAAATTTATGGAAAAAATGGACA‑GGAAAAAGGAAAAATTCCAAAAAAAGTGCGTTAATTTAGA‑TTTAGG‑TATGGGGAAAAAAAAATACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGAt                                                                                          <  1:383489/149‑1 (MQ=255)
                                             cTTTTTTATGAAGAAATTAGGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑AGTGCGGAGAATAACA‑ACCGCAGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg                                                                                            >  1:94257/1‑148 (MQ=255)
                                                ttttATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaa                                                                                       >  2:585318/1‑150 (MQ=255)
                                                   tATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTACGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAgg                                                                                    >  2:354455/1‑150 (MQ=255)
                                                       aaaaaaTTATGGAAAAAAATAAAAGGAAAAAAGGAAAAATTCAAAATAAA‑GGCGTTATTTTAGAGATTAGG‑ATTGCGGAAAAAACCA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa                                                                                <  1:201470/147‑1 (MQ=255)
                                                       aaaaaaTTAGGAAAAAAAATGAAAGGAAAAAAGGAAAAATTCAAAAAAAA‑TGCGGTACATTAGAGATAAGG‑ATGGCGAAAAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGt                                                                                 <  2:5890/146‑1 (MQ=255)
                                                           aaTTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtg                                                                           >  2:219221/1‑151 (MQ=255)
                                                               aTGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ATCGCAGTTCTCATCGAGAAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGa                                                                        >  1:298943/1‑150 (MQ=255)
                                                                gggAGAAAATGGACAGAAAAAAAGGATAATGTCTAAAGAAT‑GGTGGAAACTTAGATTTTAGT‑TGGTGGGGGAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAccag                                                                           <  1:377518/145‑3 (MQ=255)
                                                                   aaaaaaaCGAAAGGAAAAAAGAAAAAATCCTCAAAAAT‑TGCGTTAAATTAGAAATAAGA‑ATTGGGGAGAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaaa                                                                    <  2:404516/148‑1 (MQ=255)
                                                                            aCAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCt                                                          >  2:61524/1‑151 (MQ=255)
                                                                                ggAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAGGATGCAATCTATCg                                                      >  2:115859/1‑151 (MQ=255)
                                                                                  aaaaaGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGt                                                     >  1:533926/1‑150 (MQ=255)
                                                                                    aaaGGAAAAATTCTAAAAAAA‑TGCGGTAACTTAGAAATTAGG‑ATGGGGGAAAAAAAAA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACt                                                  <  2:505038/151‑1 (MQ=255)
                                                                                    aaaGAAAAAATTATAAATAAA‑GGCGTTATCAAAGAGATAGGG‑ATTGCGAAAAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACt                                                  <  1:235573/151‑1 (MQ=255)
                                                                                      aggaaaactcccaaaTAAG‑CGCGGTATTTTAGAATTTGGG‑TCTTCGGAAAATACCA‑GCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTc                                                 <  2:266048/137‑1 (MQ=255)
                                                                                      aGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCg                                                >  2:339241/1‑151 (MQ=255)
                                                                                         aaaaaTTCTAAATAAA‑GGCGGTAATTAAGAGATTAGG‑ATTGGGGAAAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCa                                              <  2:207888/148‑1 (MQ=255)
                                                                                               tctcAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTccc                                       >  1:377119/1‑151 (MQ=255)
                                                                                                   aaTAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGt                                   >  1:437573/1‑151 (MQ=255)
                                                                                                            cgttAACTAAGAGATGAGG‑TTGGCGAAAAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGt                             <  1:130590/146‑1 (MQ=255)
                                                                                                            cGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCg                           >  1:512486/1‑151 (MQ=255)
                                                                                                                          ttAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAACGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgca                >  1:201369/1‑148 (MQ=255)
                                                                                                                              g‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAgg         >  1:51022/1‑151 (MQ=255)
                                                                                                                                aTTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGc        >  2:111744/1‑151 (MQ=255)
                                                                                                                                   ggggAAAAAAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTg      <  2:263454/148‑1 (MQ=255)
                                                                                                                                     ggAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCgg   >  1:238357/1‑151 (MQ=255)
                                                                                                                                      gagaATAACA‑ACCGCCGTTCTCCTCGAGTAATCCCCGGATATCGACCCATAACGGCCACTGCTAAAAGGAGTAACCTGTGAAAAAGAAGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCg    >  1:597271/1‑149 (MQ=255)
                                                                                                                                       agaATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGa  >  1:573934/1‑150 (MQ=255)
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TATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAA‑TGCGGTAACTTAGAGATTAGG‑ATTGCGGAGAATAACA‑ACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGA  >  NC_000913/5025‑5307

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑