Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,593	0	G	C	42.5%	73.2 / 17.1	40	noncoding (60/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base G (8/15);  new base C (17/0);  total (25/15)
Fisher's exact test for biased strand distribution p-value = 1.26e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAAATCGCGCGTT  >  NC_000913/1097468‑1097741                                                                                                                              |                                                                                                                                                       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)                                                                                                                            ccGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAAATCGCGCGtt  <  2:355793/151‑1 (MQ=255)                                                                                                                              |                                                                                                                                                       GCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTG‑CTCCTTCAGCCACTCGGACACCTCA‑CCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAAATCGCGCGTT  >  NC_000913/1097468‑1097741

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑