Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,031,030	0	A	.	70.8%	9.3 / 21.7	24	coding (36/213 nt)	SAUSA300_RS10220	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (7/0);  new base . (16/1);  total (23/1)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

TCGAAATTCTCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGT  >  NC_007793/2030947‑2031111                                                                                    |                                                                                  tcgccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTg                                                              >  1:962326/10‑100 (MQ=2)  cgccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGt                                                             >  1:4690889/9‑100 (MQ=2)  cgccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGt                                                             >  1:1906654/9‑100 (MQ=2)  cgccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGt                                                             >  1:1010248/9‑100 (MQ=2)  cGAAATTCTCTGTGTGGGGGCCCACACCCCAACTTGCATTGTCTGGAGAAATTAGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTg                                                                  >  1:2467648/1‑100 (MQ=255)  aaccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGt                                                             >  1:3225372/9‑100 (MQ=2)   cccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGtt                                                            >  1:370284/8‑99 (MQ=2)   cccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGtt                                                            >  1:3182149/8‑99 (MQ=2)    tcagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCGTTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGttg                                                           >  1:3236107/7‑98 (MQ=0)    ccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGttg                                                           >  1:213625/7‑98 (MQ=2)    ccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGttg                                                           >  1:3262081/7‑98 (MQ=2)    ccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGttg                                                           >  1:372385/7‑98 (MQ=2)    ccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGttg                                                           >  1:501858/7‑98 (MQ=2)    ccagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGttg                                                           >  1:1020098/7‑98 (MQ=2)     cagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCTAACTTGCATTGTCTGttgg                                                          >  1:1163256/6‑97 (MQ=2)     cagcttctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGttgg                                                          >  1:2243014/6‑97 (MQ=0)         ctctGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTAGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAg                                                           >  1:5751780/1‑100 (MQ=17)           ctGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTAGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGaa                                                         >  1:2490974/1‑100 (MQ=17)           ctGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTAGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGaa                                                         >  1:197526/1‑100 (MQ=17)           ctGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTAGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGaa                                                         >  1:833364/1‑100 (MQ=17)           ctGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTAGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGaa                                                         >  1:87875/1‑100 (MQ=17)           ctGTGTT‑GGGCCC‑CACCCCAACTTGCATTGTCTGTTGAAATTGGTGATCCTATTTCTCTCTGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGTTGGAATTgg                                                    >  1:360940/1‑100 (MQ=2)             gtgtTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTAGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAAt                                                       >  1:1960204/1‑100 (MQ=11)                                                             agtaTTTCTTTATGTTGGGGCC‑‑CACCCCAACTTGCATTGTCTGTAGAAATTGGCGTTCCAATTTCTCTATGTTGGGGCCC‑‑‑CGCCAACTTGCATTGTCTGt  <  1:5268086/97‑1 (MQ=14)                                                                                    |                                                                                  TCGAAATTCTCTGTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGT  >  NC_007793/2030947‑2031111

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑