Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	42.3%	85.3 / 17.4	52	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (7/23);  new base G (22/0);  total (29/23)
Fisher's exact test for biased strand distribution p-value = 8.45e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAA  >  NC_000913/1097442‑1097731                                                                                                                                            |                                                                                                                                                        gTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAccccc                                                                                                                                              <  2:346528/151‑1 (MQ=35)     aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTCGGcccccccct                                                                                                                                           >  1:378049/1‑147 (MQ=255)      cGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATAc                                                                                                                                         <  1:109480/151‑1 (MQ=39)                 aCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGtata                                                                                                                              <  2:349121/151‑1 (MQ=255)                  cTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGAACCCCCCCTACGTTTCCGtata                                                                                                                              >  2:923402/1‑150 (MQ=11)                   tGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCCCTAAGTTTCCGgat                                                                                                                               >  2:332568/1‑148 (MQ=11)                    ggCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATacac                                                                                                                           <  2:4778/151‑1 (MQ=255)                          cGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTGCCGGATACACACctt                                                                                                                      >  2:475888/1‑150 (MQ=255)                           gCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGAACCCCCCCTACGTTGCCGCATACACAATTTcc                                                                                                                    >  2:632762/1‑151 (MQ=14)                             cAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCCCACCCCCCCTACGTTGCCCCATaca                                                                                                                            >  1:277722/1‑141 (MQ=11)                               gTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGc                                                                                                                <  1:18514/151‑1 (MQ=255)                                       aCCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGGGGGGGGGGTTCGAAACCCCCATACGTTGCCGTATAAAAACTTTTCCGGCGGGCTcc                                                                                                         >  1:321461/1‑150 (MQ=17)                                            ggTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGGTCGAACCCCCCATACGTTGCCGTATACAAACTTTTCCGGCGTGCTCCtt                                                                                                       >  2:208744/1‑147 (MQ=17)                                                         cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGacac                                                                                        <  1:325911/149‑1 (MQ=255)                                                                  ggTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTCGAACCCCCCGTACGTTGCCGGATACACACTTTCCCGGCGGGCGCCCTCAGCCCCTCCGGCACCCCACCaaa                                                                               >  2:31460/1‑149 (MQ=14)                                                                        tgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCGATACGTTTCCGTATACACACTTTTCAGGCGTGCTCCTTCAGCCACCCGGACACCCCACCCAAATTTCGtt                                                                       >  2:638231/1‑151 (MQ=14)                                                                        tgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGAAACCCCCATACGTTGCCGTATAAACACTTTTCCGGCGGGGTCCTTCCGCCACTCCGGCACCCCCCCaaaattttgtt                                                                       >  1:715745/1‑143 (MQ=14)                                                                         gCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTGCCGTATAAACACTTTTCAGGCGGGGTCCTTCAGCCCCCCGGACACCCCCCCAAAATTTCGtt                                                                       >  1:407193/1‑150 (MQ=14)                                                                                aCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCCATACGTTGCCGTATAAACACTTTCCAGGCGTGCTCCTTCAGCCACCCGGACACCCCCCCAAATTTTCGTTCCCGTCtt                                                               >  2:578810/1‑151 (MQ=14)                                                                                 cGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGCGAGGGGGGGGTTTGAAACCCCCATAAGTTGCCGTATACACACTTTTCAGGCGTGCTCCTTCCGCCACTCGGACACCTCACCAAATTTTCCTTCCTTTCtt                                                               >  2:702063/1‑150 (MQ=11)                                                                                   aaaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCt                                                            <  1:831435/151‑1 (MQ=255)                                                                                   aaaaaaaaG‑CCGTACCTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCtt                                                               <  2:236653/147‑1 (MQ=255)                                                                                      aaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTTGAACCCCCCCTACCTTTCCGTATACACACTTTCCCGGGGTGGTCCTTCAGCCACCCCGGCACCTCCCCCAACTATTGTTCCTTTTTTTCTgg                                                          >  1:316285/1‑150 (MQ=2)                                                                                       aaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCCCACGGTTCCGTATACACACCTTTCAGGGGTGCTCCTTCCGCCACTCCGACACCTCCCCAACATTTCGTTTCTGTTTTTCttg                                                          >  2:507294/1‑147 (MQ=2)                                                                                          aGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACgg                                                     <  2:658505/151‑1 (MQ=255)                                                                                            cccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTCGAACCCCCCATACGTTGCCGTTTAAACACTTTCCAGGCGTGCTCCTTCCGCCACTCGGGCACCTCACCCAATTGTCGTTGCTGTCTTTCTTGAACggg                                                    >  1:583192/1‑150 (MQ=14)                                                                                                 aCTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGATTCGCACCCCCGCTAACTTTCCGGAGACACACTTTCCTGGCCTGCTCCCTTCGCCACCCTGACCCCCCACCCAAATTTCGGTGCTGGCTTGGCGGGACggg                                                    >  2:963606/1‑145 (MQ=2)                                                                                                    ttCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑t                                            <  2:655960/149‑1 (MQ=255)                                                                                                    ttCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑t                                            <  1:775509/149‑1 (MQ=255)                                                                                                      cGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTa                                         <  1:428756/150‑1 (MQ=255)                                                                                                        tACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCCTACGTTTCCGTATACACACTTTCCCGGCGTGCTCCTTCCGCCACTCGGACACCCCACCACATTTTCGTTTCTGTCTTTCTGGAACGGGGGCTAA‑TTTTggg                                      >  1:884144/1‑151 (MQ=14)                                                                                                          cGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTTGAAACCCCCCTACGTTTCCGTATTCACACTTTCCCGGGGGGCTCCCTTCGCCCCTCCGGCCCCCCACCCAAATTTTGTTTCTGTCTTTCTGGGACCGGGGCTTA‑tttttgg                                      >  1:434521/1‑145 (MQ=2)                                                                                                               tcttctTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCATACGTTTCCGTATACACACTTTTCCGGCGGGGTCCTTCCGCCACTCCGACACCCCACCAAAATTTCGTTCCTGTCTTTCTGGGACGGGCGCTAA‑TTTTGGGGAAACa                                >  1:223899/1‑150 (MQ=17)                                                                                                                  tcttTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCAt                               <  1:517765/148‑1 (MQ=255)                                                                                                                    tttAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCATAAGGTTCCCTATAAACACTTTTCAGGCGTGCTCCTTCCACCCCCCCGACACCTCCCCCAAATTTCGGTTCTTTCTTGCTGGGAACGGCGCTAATTTTAGGGAAAtatgaac                            >  2:62046/1‑144 (MQ=9)                                                                                                                    tttAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCGATACCTTGGCGGATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCCCACCAAAATGTCGTTTCTGTCTTTCTGGAACGGGGGCTAA‑TTTAGGGAAAACATGAcc                           >  2:493571/1‑150 (MQ=18)                                                                                                                     ttAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCt                          <  1:9924/150‑1 (MQ=255)                                                                                                                       aaaTATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAg                       <  2:262787/151‑1 (MQ=255)                                                                                                                           atGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAgg                      >  1:476135/1‑148 (MQ=255)                                                                                                                           atGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTca                   <  1:35906/151‑1 (MQ=255)                                                                                                                            tGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTca                   >  1:906911/1‑150 (MQ=255)                                                                                                                             ggCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTcaa                  <  1:33624/150‑1 (MQ=255)                                                                                                                              gCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTcaac                 >  2:57442/1‑150 (MQ=255)                                                                                                                               cGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTcaacaa               <  1:838444/151‑1 (MQ=255)                                                                                                                                ggTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTcaacaa               >  1:788608/1‑150 (MQ=255)                                                                                                                                ggTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTcaacaa               >  2:904426/1‑150 (MQ=255)                                                                                                                                   gAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACtt           <  2:86720/151‑1 (MQ=255)                                                                                                                                   gAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACt            <  1:553882/150‑1 (MQ=255)                                                                                                                                      ggggggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACttttt        <  1:103800/151‑1 (MQ=255)                                                                                                                                         gggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaa     <  1:740973/151‑1 (MQ=255)                                                                                                                                         gggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaa     <  1:846574/151‑1 (MQ=255)                                                                                                                                          cgATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaa     >  1:553368/2‑150 (MQ=255)                                                                                                                                            aTTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaaaa  <  1:208741/151‑1 (MQ=255)                                                                                                                                            aTTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaaa   >  2:871686/1‑150 (MQ=255)                                                                                                                                            |                                                                                                                                                        GTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAA‑TTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAA  >  NC_000913/1097442‑1097731

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑