Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,536,2120TA43.6% 50.8 / 16.5 39intergenic (+181/+402)yjhR/nanSpseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
Reads supporting (aligned to +/- strand):  ref base T (2/20);  new base A (17/0);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 3.35e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGTA  >  NC_000913/4536062‑4536360
                                                                                                                                                      |                                                                                                                                                     
gtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAAt                                                                                                                                                       <  2:508762/151‑1 (MQ=255)
        cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCTCTTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTATGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaagcaa                                                                                                                                               <  1:518936/151‑1 (MQ=255)
        cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaagcaa                                                                                                                                               <  2:376549/151‑1 (MQ=255)
        cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaagcaa                                                                                                                                               <  1:297614/151‑1 (MQ=255)
             tttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCaataat                                                                                                                                           <  1:30998/150‑1 (MQ=255)
                  cAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGCTTTTTGAATGAAAAAAAAAAAAAACAaaaatataa                                                                                                                                       >  2:520673/1‑149 (MQ=255)
                    aTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATaataat                                                                                                                                  <  1:51733/151‑1 (MQ=255)
                     ttttAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATaataat                                                                                                                                  <  1:416227/148‑1 (MQ=255)
                       ttAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGAAAAAAAAAACAAACAAAAATAtaataa                                                                                                                                    >  2:521476/1‑147 (MQ=255)
                         aaGGCGACTTTCCGTTTTAATGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGTGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCt                                                                                                                             <  1:535020/151‑1 (MQ=255)
                          aGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAAAGCAAGCAATAATATAATAATGGCCt                                                                                                                             >  2:397325/1‑150 (MQ=255)
                                    ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGa                                                                                                                  <  1:196128/151‑1 (MQ=255)
                                       ttttATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGAAAAAAAAAGCAAGCAATAATATAAAAAAAGCCCAATttttttt                                                                                                                   >  2:342314/1‑146 (MQ=255)
                                        tttATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAAAGAAAGAAAAAGAAAGAAATAAAATAATAAAGGGCCAATTTCTTTGGAca                                                                                                               >  2:264918/1‑150 (MQ=255)
                                             tGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAAAAAAAACAAAAAATAATATAATAAAAGCCCAATTTTTTTGTAcaata                                                                                                            >  2:292621/1‑145 (MQ=255)
                                                     gCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAAAAAAAACAAACAATAATATAAAAAAAGCCTAATTTTTTTTTACATCATTTAGCata                                                                                                   >  2:39786/1‑149 (MQ=255)
                                                        tttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGCCGCCTTTTTGAATTAAAAAAAAAGCAACCACAAATATCAAAATCGCCCACTTTTTTTTAAcatctctaaa                                                                                                       >  1:186816/1‑136 (MQ=255)
                                                           ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatcat                                                                                            <  2:52214/150‑1 (MQ=255)
                                                               aTTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGGAATGAAAGAAAAAAAAAGCAAAAATATAAAAAAGGGCTCAATTCTTTTTACATCATTAAGAATAACATCATCCTc                                                                                        >  2:247688/1‑150 (MQ=255)
                                                                ttATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAAAAAAAACAAGCAATAATATAATAATTGCCTAATTTTTTTTTAAATCATTAAACATATCATCATCg                                                                                          >  2:61184/1‑147 (MQ=255)
                                                                  ataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTaat                                                                                    <  1:30069/151‑3 (MQ=255)
                                                                  ataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTAtt                                                                                    <  2:96663/151‑1 (MQ=255)
                                                                   taAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTTTTTTTTGGAAAGAAAAAAAAAGCAAACAATAAAATAATAAATGGCTAATTTTTTTTTAAATCATTTAACAAATCATTATCCTCTAttt                                                                                   >  2:175536/1‑151 (MQ=255)
                                                                    aaaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGGGATTAAAAAAAAAACAAACAAAAATATAATAAAGGGCTAATTTTTTTTAAAAACATTAAAAAAATCATCAATGTCTAtttt                                                                                  >  2:27942/1‑150 (MQ=255)
                                                                               tgtACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATAAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATcc                                                                         <  1:510264/147‑1 (MQ=255)
                                                                                          aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAt                                                            <  2:108018/151‑1 (MQ=255)
                                                                                          aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTTGAATGCAAGAAAAAGAAAGCAAAAAAAAAATAATTGGCCTATTTTTTTGTAAATAAATTAACAAATCATCATCCTCTATTTGCCAGTAttcctggattcat                                                               >  1:652531/1‑136 (MQ=255)
                                                                                          aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGAAAGAAAAAGCAAGCAAAAATATAATAAAAGGCTAATTTTTTTTAACAACATTAAACATATCATCATCGTCTATTTTTCAGAATACGTCGACTTATaa                                                             >  2:457807/1‑150 (MQ=255)
                                                                                               ccTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGGGATGAAAGAAAAAACAAGCCAAAATATAAAAAATGCCTAATTTTTTTTAAAATCATTAAACATATCATCATCGTCTATTTTCCCGAAACCGTCCACTTATAAttacc                                                        >  2:446232/1‑146 (MQ=255)
                                                                                                       tAATGCGCCTGGGATTAATGGCGGGGGCGTTTTTGAATGAAAAAAAAAACAAGCAAAAAAATAATAAAAGGCTAATTTTTTTGAAAATCATTAAACAAATAATCATCGTCTATTTGCCAGAAACCGTTGCCTTATAAAAACCAGaaa                                                   >  1:21646/1‑146 (MQ=255)
                                                                                                         aTGCGCCTGGGATTAATGGCGGGTGGTTTTTTGAATTAAAAAAAAAGCAAGCAATAATATAATAATGGCCCAATTTTTTTTAACATCATTTATAATATCATCATCGTCTATTTTTCCGAATCCGTCGCCTTATAAACACCACAAAgg                                                 >  2:674274/1‑147 (MQ=255)
                                                                                                           gcgcCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCatat                                            <  2:196613/150‑1 (MQ=255)
                                                                                                            cgcCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCa                                          <  2:367813/151‑1 (MQ=255)
                                                                                                                                 gCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCtgt                     <  1:342232/151‑1 (MQ=255)
                                                                                                                                       aGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGccc                >  2:281695/1‑150 (MQ=255)
                                                                                                                                       aGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCa               <  1:144273/151‑1 (MQ=255)
                                                                                                                                                agaaaATGCAAGCAATAATATAATAATGGCCTAATTTCTTTCAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTcc      <  1:471498/151‑1 (MQ=255)
                                                                                                                                                 gaaaATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTcc      >  2:17638/1‑150 (MQ=255)
                                                                                                                                                  aaaaTGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCa     <  1:39785/150‑1 (MQ=255)
                                                                                                                                                    aaTGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGTa  <  2:289178/151‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                                     
GTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGTA  >  NC_000913/4536062‑4536360

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: