Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009135,1590GA42.1% 32.3 / 20.0 38intergenic (+139/‑75)thrC/yaaXL‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (13/9);  new base A (0/16);  total (13/25)
Fisher's exact test for biased strand distribution p-value = 9.94e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGG  >  NC_000913/5011‑5300
                                                                                                                                                     |                                                                                                                                             
tcatcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGgaga                                                                                                                                              >  2:117882/1‑150 (MQ=255)
  atcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATa                                                                                                                                           <  2:689046/151‑1 (MQ=255)
  atcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATa                                                                                                                                           <  1:645057/151‑1 (MQ=255)
         aaaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAAccg                                                                                                                                    <  2:506696/151‑1 (MQ=255)
                ttCATTATCTCAATCGGGCGGGGTTTGTTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAAAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTtc                                                                                                                              <  2:390267/150‑1 (MQ=255)
                ttCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTtct                                                                                                                             >  2:322925/1‑151 (MQ=255)
                                 gCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAGAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCgg                                                                                                            >  1:769893/1‑151 (MQ=255)
                                              ttATGCAGCCCTGCTTTTTTAGGAAGAAATTAGGGAAAAAAATGAAAGGGAAAAAGGAAAATTTCTAAATAAATGGGGTAATTT‑AGAGATAAGGAGTGCGGAGAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCAt                                                                                                <  1:518186/150‑1 (MQ=255)
                                                      ccgggtttttttATAAAAAAATTAGGGAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAAAAAAGGGGGTAACTT‑AGAGATTGGGTTGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                                                                       <  1:121897/145‑1 (MQ=255)
                                                      cccGGTTTTTTTATGAAAAAATTATGGAAAAAAATGACAGGGAAAAAGGAGAAATTCTAAAAAAAGGCGATAATTT‑AGAGATTAGGATTGCGAAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc                                                                                         <  1:307923/149‑1 (MQ=255)
                                                      cccGGTTTTTTTAAAAAAAAATTGGGGAAAAAAAGGACAGGAAAAAAGGAAAAATTCTAAATAAATGCGTTAATTT‑AGAGATTAGGAGTGCGGGAAAAAACAGCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                                                                       <  2:765015/151‑1 (MQ=255)
                                                         ggCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg                                                                                     >  1:122950/1‑150 (MQ=255)
                                                          gttttttaaaaaaaaaaTTATGGAGAAAAAGGAAAGGAAAAAAGAAGAAATCCAAAAAAAATGGGTTAACTA‑AGAGATAAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGa                                                                                    <  2:117441/136‑1 (MQ=255)
                                                            tttttaaaaaaaaaaTTAGGGAAAAAAAGGAAAGGAAAAAAGGAAAAATTCCAAATAATGGGGTTAACTT‑GGAGATTGGGAGGGGGGAAAACACAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGa                                                                                    <  2:513707/136‑1 (MQ=255)
                                                            tttttaATGAAAAAATAAGGGAAAAAAATGACAGGAAAAAAGGAAAAATTCACAAAAAAGGGGGTAATTT‑AGAGATAGGGATTGCGGAAAACAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg                                                                                     <  2:237824/147‑1 (MQ=255)
                                                             tttttATAAAAAAATAATGGAAAAAAATGAGAGAAAAAAAGAAAAAATCCAAAAAAAGTGCGGTATCTT‑AGAGATTAGGAGGGAGAAAAATAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaa                                                                                 <  2:727540/150‑1 (MQ=255)
                                                                        aaaTTAGGAAAAAAAATGACAGGGAAAAAGGAAAAATTCTAAATAAATGCGGTAACTT‑AGAGATTAGGATTGGGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAcc                                                                      <  1:81326/150‑1 (MQ=255)
                                                                               gaaaaaaaaTGACAGGAAAAAAGGAAAAATTCTAAAAAAAGGGGTTAACTT‑AGAGATTAGGATTGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg                                                                  <  1:399907/143‑1 (MQ=255)
                                                                                 aaaaaaaTGACAGGAAAAAAGGAAAAATTCT‑AAAAAATGGCGTAAATTAAGAGATTAGGTTGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAg                                                            <  1:334266/149‑1 (MQ=255)
                                                                                  gaAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAGTCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                              >  2:188717/1‑148 (MQ=255)
                                                                                       aTGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCa                                                       >  1:244084/1‑150 (MQ=255)
                                                                                            ggggAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTAt                                                 >  1:613489/2‑151 (MQ=255)
                                                                                            aGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTAt                                                 >  1:158184/1‑151 (MQ=255)
                                                                                             ggaaaaaaGGAAAAATTCAAAAAAAAGGCGGTAACTT‑AGAGATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTa                                                  <  2:345666/146‑1 (MQ=255)
                                                                                             ggaaaaaaGGAAAAATCCTAAAAAAAGGCGGTAACTA‑AAAGATTAGGATGGGGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAAt                                                     <  2:210594/143‑1 (MQ=255)
                                                                                                aaaaaGGAAAAATTCTCAAAAATTGCGTTAACTT‑AGATATTAGGATGGCGGAGAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGt                                              <  2:94455/150‑1 (MQ=255)
                                                                                                aaaaaGGAAAAATTCACAAAAAATGCGGTAACTT‑AGAAATAAGGATGGAGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTa                                                  <  2:725266/146‑1 (MQ=255)
                                                                                                      gagaAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGc                                        >  2:389952/1‑150 (MQ=255)
                                                                                                       agaAATTCTAAAAAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCAc                                      <  1:476032/151‑1 (MQ=255)
                                                                                                         aaaTTCTAAATAAATGCGTTAATTT‑AGAGATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCAc                                      <  1:38427/149‑1 (MQ=255)
                                                                                                         aaaTTCTAAAAAAATGCGGTAATTT‑AGAGATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACt                                     <  1:534104/150‑1 (MQ=255)
                                                                                                                cAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTgg                             >  1:562623/1‑151 (MQ=255)
                                                                                                                  aaaaaTGCGGTAATTT‑AGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                               <  2:538852/145‑1 (MQ=255)
                                                                                                                  aaaaaGGCGGTAACTT‑AGAGATAAGTATTGCGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTccc                                <  2:429799/144‑1 (MQ=255)
                                                                                                                  aTAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCAGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGtt                           >  2:754936/1‑151 (MQ=255)
                                                                                                                      aTGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTgg                       >  1:491325/1‑151 (MQ=255)
                                                                                                                           gTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCt                  >  1:625159/1‑151 (MQ=255)
                                                                                                                                         tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgcagca      >  2:439833/1‑150 (MQ=255)
                                                                                                                                                  ggAGAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAgg  <  1:207011/145‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                             
TCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGG  >  NC_000913/5011‑5300

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑