Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	705	0	A	T	50.0%	‑5.9 / 23.1	20	A142A (GCA→GCT)	SAUSA300_RS14705	replication protein
Reads supporting (aligned to +/- strand):  ref base A (9/1);  new base T (9/1);  total (18/2)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

ATGGCAAAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATGAAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTT  >  NC_007790/612‑803                                                                                              |                                                                                                   aTGGCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAc                                                                                         >  1:1468365/1‑100 (MQ=255) aTGGCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAc                                                                                         >  1:5687566/1‑100 (MQ=255) aTGGCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAc                                                                                         >  1:3043883/1‑100 (MQ=255)   ggCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAcat                                                                                       >  1:5963664/1‑98 (MQ=255)   ggCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAcag                                                                                       >  1:1837706/1‑98 (MQ=255)                      tacttATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAatc                                                                    >  1:2957014/5‑100 (MQ=255)                              gACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGact                                                            >  1:1477282/1‑98 (MQ=255)                                                                  taaaaGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATGAAAAAAATCAAGa                             >  1:5833852/2‑100 (MQ=255)                                                                   caaaGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATGAAAAAAATCAAGaa                            >  1:104/2‑100 (MQ=255)                                                                         agATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATGAAAAAAATCAAGAAAttatc                      <  1:4542502/99‑4 (MQ=255)                                                                                        tataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaag       >  1:221725/6‑99 (MQ=255)                                                                                         ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg      >  1:890634/5‑98 (MQ=255)                                                                                         ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg      >  1:2862335/5‑98 (MQ=255)                                                                                          taacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggt     >  1:2750975/4‑97 (MQ=255)                                                                                          gaccAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggt     >  1:3737961/4‑97 (MQ=255)                                                                                          gaacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggt     >  1:5576103/4‑97 (MQ=255)                                                                                           aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtt    >  1:435161/3‑96 (MQ=255)                                                                                           aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtt    >  1:5702444/3‑96 (MQ=255)                                                                                           aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtt    >  1:2484140/3‑96 (MQ=255)                                                                                            acAATCAAAGAGACATCAAAATATTCCTTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAATCAAGAAATTTTTAGTGATCTAG‑AAAAGGttt  <  1:2712678/99‑1 (MQ=255)                                                                                              |                                                                                                   ATGGCAAAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATGAAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTT  >  NC_007790/612‑803

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑