Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	50.0%	35.6 / 15.9	38	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (7/12);  new base G (19/0);  total (26/12)
Fisher's exact test for biased strand distribution p-value = 3.72e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097446‑1097730                                                                                                                                         |                                                                                                                                                       aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATa                                                                                                                                         <  1:102733/151‑1 (MQ=39)       tGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGGTTGAAcccccccaaagtt                                                                                                                                     >  2:633959/1‑141 (MQ=11)                ggCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATacac                                                                                                                          <  1:650152/151‑1 (MQ=255)                ggCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATaca                                                                                                                           <  2:62482/150‑1 (MQ=255)                          aGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAgg                                                                                                                <  2:520334/151‑1 (MQ=255)                              gTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGt                                                                                                             <  1:754891/150‑1 (MQ=255)                                cGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTTGAACCCCCCCTAAGTTTGCGGATACACACTTTCCCGGCggg                                                                                                            >  1:262574/1‑147 (MQ=14)                                         gTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGGTCGGACCCCCCATACGTTGCCGTATAAACACTTTTCAGGCGTGGTCCTTCCGcc                                                                                                 >  2:446654/1‑151 (MQ=17)                                               gCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCgg                                                                                          <  1:12566/151‑1 (MQ=255)                                                  tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCCCTACGTTGCCGTATACACACTTTCCCGGCGTGCTCCCTCAGCCAC‑TCGGac                                                                                        >  1:577560/1‑150 (MQ=255)                                                           cccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGA‑GGGGGGGGATCGAAACCCCGCTACGTTGCCCTTTACACACCTTCCCGGCGGGCTTCCTCCGGCAC‑CCGGGCACCCCAcc                                                                                >  1:18362/1‑149 (MQ=17)                                                                tgtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGCGAGGGGGGGGATTCG‑ACCCCCGGTAAGTTTCCGCATTTACACTTTCAAGGCCGGCCCCTTCAGCCCC‑CCCGACAcccccaccaatttt                                                                         >  2:512411/1‑139 (MQ=9)                                                                     gCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGGTTTAACCCCCCCTACGTTTTCGTATACACAATTTCCAGGCGGGGTCCTTCAGCCAC‑CCCGACAACCCCCCAAAATTTCGt                                                                      >  2:405364/1‑149 (MQ=14)                                                                      cAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGGTCGAAACCCCCGTACGGTTCCGCATACACACTTTCCAGGCGGGCTCCTTCCGCCAC‑TCCGACACCTCACCcaa                                                                             >  1:207889/1‑141 (MQ=14)                                                                      cAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTTGAACCCCCGATACGTTGCCGGATAAACACATTCCAGGCGGGCTCCTTCAGCCCC‑TCGGGAACCCCACCCAAATTTCGtt                                                                     >  2:211055/1‑149 (MQ=14)                                                                       aaTATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCt                                                                  <  1:617803/151‑1 (MQ=255)                                                                       aaTATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCt                                                                  <  1:104054/151‑1 (MQ=255)                                                                           taCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTTGAACCCCCCCTACGTTTCCGTATAAACACTTTCCCGGCGGGGTCCTTCCGCCAC‑TCCGGCACCTCCCCCAAATTTCGtt                                                                     >  2:122141/1‑144 (MQ=11)                                                                            aCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTTGAACCCCCCATACGTTGCCGTATACACACTTTTCCGGCGTGCTCCTTCCGCCCC‑CCCGACACCTCACCCAATTTTTGTTTCTGTCt                                                              >  1:235446/1‑150 (MQ=11)                                                                              gAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGAAACCCCGCTACGTTGCCGTATACACACTTTTCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCtt                                                             >  1:493395/1‑149 (MQ=255)                                                                              gAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGGTTGAAACCCCCCTACGTTGCCGTATACACACTTTCCAGGCGGGGTCCTTCCGCCAC‑CCCGGCACCTCACCCAATTTTCGTTTCTGTCtt                                                             >  1:68429/1‑149 (MQ=14)                                                                                  aaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGAAACCCCCATACGGTGCCGTATACACACTTTTCCAGCGTGGTCCTTTCGCCAC‑CCCGGCACCTCACCAAAATTTTGTTTCTGTCTTGCTgg                                                        >  1:206609/1‑150 (MQ=14)                                                                                   aaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGAACCCCCCATAAGTTTCCGTATACACACTTTTCAGGCGTGCTCCTTCAGCCAC‑TCGGGCACCCCACCAAATTTTCGTTCCTGTCtt                                                             >  1:725677/1‑144 (MQ=14)                                                                                        cccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGAAACCCCGATACGTTGCCGGATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCCGACACCCCCCCCAAATTTCGTTCCTGTCTTGCTGGGACggg                                                  >  1:515804/1‑150 (MQ=14)                                                                                           gTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTTCCACCCCCCCTACGTTTTCCTATACACAATTTTCCGGCGTGCTCCTTCAGCCAC‑CCCGGCACCCCACCAAAATATCGTTTCTCTTTTTCTGGAAAAGgcgcc                                              >  2:738807/1‑150 (MQ=2)                                                                                           gTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGGG‑AGGGGGGGTTTGAAACCCCGGTACGTTGGCGTATAAAGACTTTCCACGGGGGTTCCCTCCGCCACACCGGAAACC‑CACCAAATTTTCGTTCCTGTCTTGCTGGAACCGgcg                                                >  2:209642/1‑149 (MQ=12)                                                                                                  cGTACGAGCTCTTCTTTAAATATGGCGGTGC‑GGGGGGGATTCGAACCCCCCACAACTTACCGACTACACACTTTTCAGGCGTTCTCCTTTAACCCC‑TCCGACCACCCACCCAACTGTAGTTCCTCTCTTCCTGGCACgg                                                   >  1:172461/1‑139 (MQ=2)                                                                                                   gTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGAAACCCCGATACGTTGCCGTATACACACTTTTCAGGCGGGCTCCTTCAGCCAC‑TCCGACACCTCCCCAAATTGTCGTTCCTGTCTTTCTGGGAAGGGGGCCCAttt                                         >  1:139545/1‑148 (MQ=14)                                                                                                     aCGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTGGAACCCCCCATACGTTTTCGTAATCACACTTTTCCGGCGTGCTCCCTTAGCCCC‑CCGGACACCTCCCCCAAATATCGTTTCTTTCTTTCTGGAACGGGCGCTCAttt                                         >  1:573386/1‑146 (MQ=9)                                                                                                        aGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGGTTCGAACCCCCCATACGTTTCCGGATACACACTTTTCAGGCGGGGTCCCTCAGCCAC‑CCCGGCACCCCCCCAAATTTTCGGTTCTGTCTTTCTGGGACGGGGGCTAATTTTGGGgaa                                  >  1:347716/1‑150 (MQ=9)                                                                                                         gCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATc                                <  2:335762/151‑1 (MQ=255)                                                                                                             ttcttTAAATATGGCGGTGA‑GGGGGGGGTTTGAACCCCCCCTACGTTGCCGTATACACACCTTCCCAGGGTGCTCCCTCAACCAC‑CCGGACACCTCACCCCAATTTCTTTTCTGTCTTTCTGGGACGGGCGCTAATTTTAGGAAATCa                               >  2:319421/1‑148 (MQ=9)                                                                                                                  tAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTg                        <  1:604862/150‑1 (MQ=255)                                                                                                                         ggCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTcaac                >  1:441944/1‑151 (MQ=255)                                                                                                                            ggTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTcaacaa              >  1:13112/1‑150 (MQ=255)                                                                                                                             gTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAAc            <  1:28909/151‑1 (MQ=255)                                                                                                                               gA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtt          >  1:556833/1‑151 (MQ=255)                                                                                                                                a‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACttt         <  1:683866/151‑1 (MQ=255)                                                                                                                                         aTTCGAACCCCCGATACGTTGCCGTATACACCCTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaaa  >  1:511428/1‑150 (MQ=255)                                                                                                                                         |                                                                                                                                                       ACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCAC‑TCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097446‑1097730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑