Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	44.7%	44.1 / 22.3	38	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
Reads supporting (aligned to +/- strand):  ref base A (1/20);  new base T (17/0);  total (18/20)
Fisher's exact test for biased strand distribution p-value = 6.25e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCA  >  NC_000913/4536052‑4536347                                                                                                                                                  |                                                                                                                                                        tACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGaa                                                                                                                                                     <  2:385270/150‑1 (MQ=255)  aCAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAAt                                                                                                                                                    <  2:658707/150‑1 (MQ=255)        gtagtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATgaaagaa                                                                                                                                             <  2:239765/151‑1 (MQ=255)          agtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGATTTTTTGAAttgaaaaaa                                                                                                                                            >  1:34369/1‑142 (MQ=255)           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)                               aTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATaataa‑t                                                                                                                     <  1:51733/151‑1 (MQ=255)                                ttttAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATaataa‑t                                                                                                                     <  1:416227/148‑1 (MQ=255)                                  ttAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGAAAAAAAAAACAAACAAAAATAtaataa                                                                                                                       >  2:521476/1‑147 (MQ=255)                                    aaGGCGACTTTCCGTTTTAATGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGTGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCt                                                                                                                <  1:535020/151‑1 (MQ=255)                                     aGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAAAGCAAGCAATAATATAATAA‑TGGCCt                                                                                                                >  2:397325/1‑150 (MQ=255)                                               ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGa                                                                                                     <  1:196128/151‑1 (MQ=255)                                                  ttttATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGAAAAAAAAAGCAAGCAATAATATAAAAA‑AAGCCCAATttttttt                                                                                                      >  2:342314/1‑146 (MQ=255)                                                   tttATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAAAGAAAGAAAAAGAAAGAAATAAAATAATAA‑AGGGCCAATTTCTTTGGAca                                                                                                  >  2:264918/1‑150 (MQ=255)                                                        tGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAAAAAAAACAAAAAATAATATAATAA‑AAGCCCAATTTTTTTGTAcaata                                                                                               >  2:292621/1‑145 (MQ=255)                                                                gCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAAAAAAAACAAACAATAATATAAAAA‑AAGCCTAATTTTTTTTTACATCATTTAGCata                                                                                      >  2:39786/1‑149 (MQ=255)                                                                   tttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGCCGCCTTTTTGAATTAAAAAAAAAGCAACCACAAATATCAAAA‑TCGCCCACTTTTTTTTAAcatctctaaa                                                                                          >  1:186816/1‑136 (MQ=255)                                                                      ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATatcatcat                                                                               <  2:52214/150‑1 (MQ=255)                                                                          aTTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGGAATGAAAGAAAAAAAAAGCAAAAATATAAAAA‑AGGGCTCAATTCTTTTTACATCATTAAGAATAACATCATCCTc                                                                           >  2:247688/1‑150 (MQ=255)                                                                           ttATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAAAAAAAACAAGCAATAATATAATAA‑TTGCCTAATTTTTTTTTAAATCATTAAACATATCATCATCg                                                                             >  2:61184/1‑147 (MQ=255)                                                                             ataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTaat                                                                       <  1:30069/151‑3 (MQ=255)                                                                             ataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTAtt                                                                       <  2:96663/151‑1 (MQ=255)                                                                              taAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTTTTTTTTGGAAAGAAAAAAAAAGCAAACAATAAAATAATAA‑ATGGCTAATTTTTTTTTAAATCATTTAACAAATCATTATCCTCTAttt                                                                      >  2:175536/1‑151 (MQ=255)                                                                               aaaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGGGATTAAAAAAAAAACAAACAAAAATATAATAA‑AGGGCTAATTTTTTTTAAAAACATTAAAAAAATCATCAATGTCTAtttt                                                                     >  2:27942/1‑150 (MQ=255)                                                                                          tgtACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATAAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATcc                                                            <  1:510264/147‑1 (MQ=255)                                                                                                     aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAt                                               <  2:108018/151‑1 (MQ=255)                                                                                                     aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTTGAATGCAAGAAAAAGAAAGCAAAAAAAAAATAATTGGCCT‑ATTTTTTTGTAAATAAATTAACAAATCATCATCCTCTATTTGCCAGTAttcctggattcat                                                  >  1:652531/1‑136 (MQ=255)                                                                                                     aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGAAAGAAAAAGCAAGCAAAAATATAATAA‑AAGGCTAATTTTTTTTAACAACATTAAACATATCATCATCGTCTATTTTTCAGAATACGTCGACTTATaa                                                >  2:457807/1‑150 (MQ=255)                                                                                                          ccTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGGGATGAAAGAAAAAACAAGCCAAAATATAAAAA‑ATGCCTAATTTTTTTTAAAATCATTAAACATATCATCATCGTCTATTTTCCCGAAACCGTCCACTTATAAttacc                                           >  2:446232/1‑146 (MQ=255)                                                                                                                  tAATGCGCCTGGGATTAATGGCGGGGGCGTTTTTGAATGAAAAAAAAAACAAGCAAAAAAATAATAA‑AAGGCTAATTTTTTTGAAAATCATTAAACAAATAATCATCGTCTATTTGCCAGAAACCGTTGCCTTATAAAAACCAGaaa                                      >  1:21646/1‑146 (MQ=255)                                                                                                                    aTGCGCCTGGGATTAATGGCGGGTGGTTTTTTGAATTAAAAAAAAAGCAAGCAATAATATAATAA‑TGGCCCAATTTTTTTTAACATCATTTATAATATCATCATCGTCTATTTTTCCGAATCCGTCGCCTTATAAACACCACAAAgg                                    >  2:674274/1‑147 (MQ=255)                                                                                                                      gcgcCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCatat                               <  2:196613/150‑1 (MQ=255)                                                                                                                       cgcCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCa                             <  2:367813/151‑1 (MQ=255)                                                                                                                                            gCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCtgt        <  1:342232/151‑1 (MQ=255)                                                                                                                                                  aGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGccc   >  2:281695/1‑150 (MQ=255)                                                                                                                                                  aGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCa  <  1:144273/151‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                        TACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAA‑TGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCA  >  NC_000913/4536052‑4536347

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: ‑