Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	48.7%	51.3 / 17.3	39	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (5/15);  new base G (19/0);  total (24/15)
Fisher's exact test for biased strand distribution p-value = 7.71e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097442‑1097730                                                                                                                                            |                                                                                                                                                        gTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAccccc                                                                                                                                              <  2:355229/151‑1 (MQ=35)                 aCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTCAcccccccccccgttttccttt                                                                                                                               >  1:450001/1‑135 (MQ=1)                           gCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCCCTACCTTGCCGTATtca                                                                                                                            >  1:393103/1‑143 (MQ=14)                              aGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAgg                                                                                                                 <  1:409558/151‑1 (MQ=255)                                  gTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                                                                             <  1:949222/151‑1 (MQ=255)                                            ggTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGGTCGAACCCCCCCTCCGTTTCCGGATACACACCTTCCCGGCGGG‑CGcc                                                                                                        >  1:336512/1‑145 (MQ=14)                                                ggggCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACt                                                                                              <  2:799225/151‑1 (MQ=255)                                                     ttCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTGGGACCCCCCCTAAGTTTCCGTATACACCCCTTCCACGCGGG‑CTCCCTCcaccaccc                                                                                             >  2:531948/1‑145 (MQ=14)                                                           tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCGCTACGTTGCCGTATACACACTTTCCCAGCGGG‑CTCCTTCAGCCACTCGGACAcccc                                                                                    >  2:942603/1‑148 (MQ=17)                                                            ccccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCa                                                                                   <  2:753679/150‑1 (MQ=255)                                                                ccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAAt                                                                            <  2:672403/151‑1 (MQ=255)                                                                 cGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCCATACGTTGCCGTATACACACTTTCCAGGCGGG‑CTCCTTCAGCCACTCCGACCCCCCA‑CCaaa                                                                             >  2:321319/1‑150 (MQ=14)                                                                  ggTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCCTACGTTTCCGTATACACACCTTTCCGGCGTG‑CTCCCTCAGCCACACGGACACCCCA‑CCcaa                                                                             >  2:614407/1‑149 (MQ=14)                                                                    tgtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTGCCGTATACACACCTTTCCGGCGTG‑CTCCTTCAGCCCCTCGGGCACCCCC‑CCAAAtttt                                                                         >  1:479983/1‑149 (MQ=14)                                                                        tgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGATTCGCACCCCCCCTACGTTGTCGTATACACACCTTCCAGGCGTG‑CTCCTTCCGCCACCCGGACACCCCACCCAAAttttgtt                                                                      >  1:390937/1‑146 (MQ=14)                                                                         gCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGtt                                                                     <  2:740458/150‑1 (MQ=255)                                                                            atatACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAATTATGGCGGTGAGGGGGGGGTTTGAACCCCCCATACGGTTCCGTATACACACTTTCCCGGCGGG‑CTCCCTCCGCCACCCCGACACCCCA‑CCCAAATTTCggt                                                                     >  2:348962/1‑145 (MQ=11)                                                                            atatACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAACCCCCCCTACGTTTCCGTATACACACTTTCCCGGCGTG‑CTCCTTCAGCCACTCGGGCCCCCCA‑CCCAATTTTCGTTcc                                                                   >  2:17005/1‑149 (MQ=14)                                                                                 cGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCCCAACGTTTCCGTATACACCCTTTTCCAGCGGG‑GCCCTTCAGCCCCCCCGGCACCCCA‑CCCAAATTTCGTTTCTCTCtt                                                             >  2:400483/1‑150 (MQ=2)                                                                                  gAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCCGTACGTTGGCGTATAAACACTTTCCCGGCGGG‑GTCCCTCAGCCCCCCGGGCACCTCC‑CCAAAATTTTGTTTCTGTCtt                                                             >  2:457754/1‑149 (MQ=11)                                                                                     aaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGAACCCCCCATACGTTGCCGTATACACACTTTTCCGGCGGG‑GTCCTTCAGCCACCCCGACACCCCC‑CCCAAATTTTGTTCCTGTCTTTCt                                                          >  2:641155/1‑149 (MQ=14)                                                                                         aaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTTCCGCTTACACACTTTTCCGGCGTGCCTCCTT‑TGCCACCCCGACACCTCA‑CCCAATTTTTGTTTCTGTCtt                                                             >  2:352223/1‑142 (MQ=9)                                                                                          aGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAGGGGGGGGTTCGAACCCCCCCTCCTTTTCCGTATACACCCTTTCCCGGCGTG‑CTCCTTCCGCCCCCCGGACACCCCC‑CCAAAATATCGTTTCTCTCTTTCTGGAACg                                                    >  1:321575/1‑150 (MQ=14)                                                                                            cccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGgc                                                 <  1:39173/151‑1 (MQ=255)                                                                                             ccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGAGTGGGGGGGTCGAACGCCCCGTAAGGTGCCCTGTTTACACCTTCCAGGCGGG‑CTCATTCACGCACCCGGAGACCCCC‑CCAAATTGTGGTTTTCGTCTTTCTTGaaat                                                    >  2:818801/1‑145 (MQ=2)                                                                                                 aCTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTaa                                            <  1:441118/151‑1 (MQ=255)                                                                                                  cTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTa                                             <  1:641048/149‑1 (MQ=255)                                                                                                   tttCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGCAACCCCCCTACGTTGCCGTATACACACTTTCCAGGCGGG‑GGCCTTCAGACACCCGGACACCCCC‑CCCCAATTTCGGTTCTTTTTTGCTGGGAAGGgcgc                                               >  1:571344/1‑146 (MQ=2)                                                                                                        tACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGAAACCCCGATACGGTGGCGTATACACACTTTCCAGGCGGG‑GTCCTTCAGCCACTCCGGCACCCCA‑CCAAATTGTCGTTTCTGTCTTTCTGGAAAGGGCGCCAATTTTggg                                     >  2:595658/1‑151 (MQ=14)                                                                                                          cGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGaa                                   <  1:36804/151‑1 (MQ=255)                                                                                                            aGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGGTTGAAACCCCCCTACTGTTTCGTATACACACCTTTCCGGGGGG‑GGCCTTCAGCCACCCCGGCACCCCACCCAAATTTTGGTT‑CTGTTTTTCTGGGACGGGCGCTCATTTTTGGaaa                                  >  1:947111/1‑150 (MQ=2)                                                                                                                     ttAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCt                         <  1:202377/150‑1 (MQ=255)                                                                                                                       aaaTATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAg                      <  2:22134/151‑1 (MQ=255)                                                                                                                         atatGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGt                    >  2:852382/1‑151 (MQ=255)                                                                                                                                ggTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACCCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACaaa             <  2:885763/151‑1 (MQ=255)                                                                                                                                  tGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACt           >  1:239684/1‑151 (MQ=255)                                                                                                                                      ggggggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACttttt       >  2:798971/1‑151 (MQ=255)                                                                                                                                         gggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGa     >  2:578942/1‑150 (MQ=255)                                                                                                                                          ggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaa   <  1:435297/151‑1 (MQ=255)                                                                                                                                            aTTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaaa  >  1:235555/1‑150 (MQ=255)                                                                                                                                            aTTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaa   >  2:736192/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                        GTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097442‑1097730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑