Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	66.7%	5.8 / 14.2	18	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (1/5);  new base G (12/0);  total (13/5)
Fisher's exact test for biased strand distribution p-value = 7.00e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.20e-03

CGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097441‑1097730                                                                                                                                               |                                                                                                                                                      cGTTCACGGTCTCTCCACCCGGCTGTGGCCTGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGATTc                                                                                                                                                    <  1:154301/144‑1 (MQ=255)                                      gAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTc                                                                                                        <  1:187124/151‑1 (MQ=255)                                           ccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGGTTCAAACCCCCCA‑ACGTTTCCCTATAAACACCTTTCAGGGGGGCTccct                                                                                                     >  1:522670/1‑147 (MQ=11)                                              gTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGGTTCGAACCCCCCCTACGTTGCCGTATAAACACTTTCCCGGCGGGCTCCTTCCGcc                                                                                                >  2:221090/1‑151 (MQ=18)                                              gTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGATTCGAACCCCCGATACGtt                                                                                                                                    <  2:216392/115‑1 (MQ=255)                                                          cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGAGAA‑GGGGGGGGTTTG‑ACCCCCGCAGAGCTGCCGGATAAACACTTTCCCGGAGGGGTCCTTCAACCGCCCGGacaac                                                                                     >  2:219960/1‑148 (MQ=2)                                                                    gtgtgtGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTT‑G‑GGGGGGGGGTCGAAACCCCCATACCTTTCCGTATACACAACTTCCCTGCGGGGTCCTTTATCCACCCGGCCAACTcccccca                                                                             >  1:538974/1‑145 (MQ=9)                                                                              tataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑G‑GGGGGGGGTTTGGACCCCCCCTACGTTTCCGCCTTAACACTTTCCCAGCGGGCTCCTTCCGCCCCCCGGTCACCCCCCCCAATTTTCGTTcc                                                                   >  2:103650/1‑148 (MQ=9)                                                                                 aCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGGGTTGAACCCCCCCTACGCTTCCGGATAAACACTTTCCACGCGTGCTCCCTCCACCACTCCGACACCCCACCACAATGTTGTTTCTGTCtt                                                             >  2:465829/1‑151 (MQ=14)                                                                                    aaaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGG‑A‑GGGGGGGGGTTGAACCCCCCCTACGTTTCCGTATTAAAACCTTCCAGGGGGGCTCCCTCAGCCCCCCCGACACCCCCCCCAAATTTTGTTCCTTTCtt                                                             >  1:398275/1‑148 (MQ=2)                                                                                              ccGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGGTTTCAACCCCCCACACCTTGCCTCATTTACACCTTTCCGGCGTGCGCCTTCTGCCACCCCGGCACCTCCCCACAATGTCGGTCCTGCTTTTCTGGGAAggg                                                  >  1:316422/1‑149 (MQ=2)                                                                                                      tCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGGGTTGGACCCCCCACACCTTGCCGTATAAACACTTTTCCGGCGGGCTCCTTCCGCCCCCCGGGCACCCCCCCCAAATTTCGTTCCCGTCTTTCTGGAACGGGCGCCAAttt                                         >  1:142811/1‑150 (MQ=9)                                                                                                        gTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGGGTTGAACCCCCCCTACGTTGCCGTATACACACTTTTCCGGCGGGCTCCTTCAGCCACCCCGACACCCCCCCCAATTTTCGTTCCTGTCTTGCTGGGAAGGGCGCTAAtttttg                                      >  2:51769/1‑148 (MQ=17)                                                                                                              gCTCTTCTTTAAATATGGCGGGG‑A‑GGGGGGGGGTTGAACCCCCCATAACTTTCCGTATACACACTTTTCAGGCGGGCTCCTTCCCCCACCCGGGCACCCCACCCAAATTTCGTTCCTGTCTTTCTGGAAAGGGCGCTAATTTTGGGaaaac                                >  1:292145/1‑149 (MQ=12)                                                                                                                         aaTATGGCGGTG‑A‑GGGGGGGGGTTGAACCCCCGATACGATGGCGTATTAACACTTTTCAGGCGGGGTCCTTCAACCACACCGACACCCCACCAAATTATCTGTCCTGTCTTTCTGGAACTGGCGCCACTTTTGGGGAAAAATGACCt                         >  1:331149/1‑147 (MQ=9)                                                                                                                          atatGGCGGTG‑A‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAgg                     >  1:551187/1‑150 (MQ=255)                                                                                                                                    g‑A‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtt          <  2:377655/151‑1 (MQ=255)                                                                                                                                         ggggggATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACttttt       <  2:419334/151‑1 (MQ=255)                                                                                                                                               aTTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaaaa  >  2:241237/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                                      CGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑A‑GGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAA  >  NC_000913/1097441‑1097730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑