Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	43.2%	44.1 / 35.8	44	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 (2/23);  new base T (19/0);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.49e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCC  >  NC_000913/4536047‑4536345                                                                                                                                                        |                                                                                                                                                       cATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTa                                                                                                                                                        <  2:426782/151‑1 (MQ=255) cATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTa                                                                                                                                                        <  2:689806/151‑1 (MQ=255)     aTACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAAGCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGa                                                                                                                                                     <  1:350333/150‑1 (MQ=255)       aCAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATg                                                                                                                                                  <  1:517342/151‑1 (MQ=255)        cAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATga                                                                                                                                                 <  1:35353/151‑1 (MQ=255)          ggAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTATGAATgaaa                                                                                                                                               <  2:401588/151‑1 (MQ=255)            agtagtAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATgaaaga                                                                                                                                             <  2:707253/151‑1 (MQ=255)              tagtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTAGGaagaaaaaa                                                                                                                                             >  2:694589/1‑143 (MQ=255)                  aaaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATgc                                                                                                                                       <  1:371686/151‑1 (MQ=255)                    aGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATgcaa                                                                                                                                     <  2:7687/151‑1 (MQ=255)                     gggCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATgcaag                                                                                                                                    <  2:618538/151‑1 (MQ=255)                       gCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATgcaagca                                                                                                                                  <  2:553519/151‑1 (MQ=255)                       gCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATgcaagca                                                                                                                                  <  1:176272/151‑1 (MQ=255)                        cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTATTGGC‑GGTTCCTTTTATGAATGAAATAAAATgcaagcaa                                                                                                                                 <  2:247169/151‑1 (MQ=255)                        cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGCTTTTTGGAATGAAAGAAAAAgcaa                                                                                                                                     >  1:70330/1‑147 (MQ=255)                                aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAataatataa                                                                                                                         <  2:85200/151‑1 (MQ=255)                                aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTGGAATGAAAGAAAAAGGAAGCaataa                                                                                                                              >  1:490370/1‑146 (MQ=255)                                 ccAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTGGAATGAAAGAAAAAGCAAGCCaaaatataa                                                                                                                         >  1:141036/1‑150 (MQ=255)                                    aTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTTGGAAGAAAAAAAAAGAAAACAAAAAAAtaataa                                                                                                                      >  1:111410/1‑150 (MQ=255)                                     tGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGGATGAAAAAAAAAGCAAACAAAAAAAtaaaaa                                                                                                                      >  1:135281/1‑149 (MQ=255)                                     tGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGAGTTAAAAAAAAAACAAGAAAaaatataata                                                                                                                       >  2:253578/1‑148 (MQ=255)                                              gACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGGATGATAGAAAAAGCCAGCCAAAAATTAATAAT‑AGcgt                                                                                                               >  1:435743/1‑144 (MQ=255)                                                    ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTGGAATGAAAAAAAAAACAAAAAATAATATAAAAAA‑AGGCTAA‑Ttttttttt                                                                                                   >  1:494777/1‑149 (MQ=255)                                                     cGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGaa                                                                                                  <  1:421436/151‑1 (MQ=255)                                                      gTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAAc                                                                                                 <  1:240296/151‑1 (MQ=255)                                                        tttATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGCTTTTTTGAATGAAAAAAAAAAAAAACAAAAATATAAAAAA‑AGCCTAA‑Tttttttttaaa                                                                                                >  1:129565/1‑145 (MQ=255)                                                            ttGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGCTTTTTTGATTTGAAAAAAAAACTAGACAAAATATAATAAA‑TGCCTAA‑Tttttttt                                                                                                    >  2:372330/1‑141 (MQ=255)                                                              gCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGGTTTTTTGTATGAAAAAAAAAGCAAGCAATAATATAATAAA‑GGGCTAA‑TTTTTTTTTACATCATTa                                                                                          >  1:139072/1‑150 (MQ=255)                                                               cGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAg                                                                                        <  2:299644/151‑1 (MQ=255)                                                                             tGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGAATGAAAAAAAATACCAGCAATAAAAAAATAAA‑GGCCTCA‑TTTTTTTTAACATAATTAAAAATATCATCAACGt                                                                          >  2:364991/1‑151 (MQ=255)                                                                                 tataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGGTTTTTGGAATGAAAAAAAAAACAAACAATAAAATAAAAAA‑AGGCTAA‑TTTTTTTTAAAATCATTTAACATATCATCATCGTCttt                                                                      >  1:227806/1‑149 (MQ=255)                                                                                    aaaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGTTTTAAAAAAAAAACAAAAAAAAAAATAAAAATAGGCTTTA‑TTT‑TTTTTACAACATTAAACACATAATTATTTTCTAtttt                                                                   >  2:111878/1‑150 (MQ=255)                                                                                    aaaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTg                                                                   <  1:250696/151‑1 (MQ=255)                                                                                             tGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGCTTTTTGG‑ATGAAAAAAAAATCAAACAAAAAAAAAAAAAA‑AGGCTAA‑TTTTTTTTAAAAACATTTAAAATATTATCATCGTCTttttttcataa                                                             >  1:20570/1‑141 (MQ=255)                                                                                              gTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATcc                                                          <  1:719115/150‑1 (MQ=255)                                                                                                    cTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTTGAATGAAAAAAAAAACAAACAAAAAAATAATAAA‑AGGCTAATTTTTTTTTAACA‑CAATAAACAAATTATTATCGTCTATTTTCCAGAAACCCTc                                                       >  1:468513/1‑147 (MQ=255)                                                                                                    cTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGCTTTTTGGAATTGAAGAAAAAGGAAGCAATAATATAATAAT‑GGGCTAA‑TTTTTTTTAAAATCATTAAACATATTATTATCGTCTATTTTCCAGAATcc                                                          >  1:91000/1‑144 (MQ=255)                                                                                                      aaTCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACt                                                   <  2:564597/149‑1 (MQ=255)                                                                                                                   tGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGGATGAAAAAAAAAACAAGCAAAAATATAAAAAA‑AGGCTAA‑TTTTTTTTAAAATCATTAAACATATCATAATCGTCTATTTTTCAGAATCCGTCGACTTTTAATCCCCAGaa                                     >  1:310497/1‑150 (MQ=255)                                                                                                                    gCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGACAGaat                                    <  2:96236/150‑2 (MQ=255)                                                                                                                      aTAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTGGAATGAAAAAAAAAGCAAACAAAAAAATAAAAAA‑AGGCTAA‑ATTTTTTTAAAATCATTTAACATAATATCATCGTCTTTTTTCCAGAATCCGTCGACTTATAAATTCCCGAACgg                                  >  1:698836/1‑150 (MQ=255)                                                                                                                         aTGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCata                              <  2:356612/151‑1 (MQ=255)                                                                                                                                       aaTGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGtgctg                <  2:234717/151‑1 (MQ=255)                                                                                                                                       aaTGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGtgct                 <  1:432120/150‑1 (MQ=255)                                                                                                                                               ggTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGCCTTATAATCGCCAGAGCGGCATATCAGGACGGTGCTGCGAACGc         <  2:473901/151‑1 (MQ=255)                                                                                                                                                      ttAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGcc  >  1:476317/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                       CATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAAT‑GGCCTAA‑TTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCC  >  NC_000913/4536047‑4536345

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑