Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,604,207	0	C	A	76.5%	23.8 / 3.7	17	S408R (AGC→AGA)	SAUSA300_RS13380	transporter
Reads supporting (aligned to +/- strand):  ref base C (3/1);  new base A (13/0);  total (16/1)
Fisher's exact test for biased strand distribution p-value = 2.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01

GTTAAAGGTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTT‑A‑‑ATCGGAAGCGCATCGGCTAAATGGGGTATTTTAGGACCGATATTCGTACCAATGTTAATCCTTATCGGCTTTC  >  NC_007793/2604112‑2604271                                                                                                   |                                                                 gTTAAAGGTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAGCATGTA‑G‑‑ATCGGAAGAGCac                                                              >  1:4457959/1‑99 (MQ=255)  gtAAAGGTGCCAAATTATTAGAACATCAAAACGGTATTCTATTGATACTAGGCATTATTGTACTGAGTGCAATGGTCAACATGCA‑G‑‑ATCGGAAGAGCaca                                                             >  1:2064238/2‑98 (MQ=255)    acaGGTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTT‑A‑‑ATCGGAAGCGCATCgg                                                           >  1:342978/3‑100 (MQ=255)     taGGTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAATATGTT‑AG‑ATCGGAAGAGCacacg                                                           >  1:3580898/2‑96 (MQ=255)     aaGGTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGAC‑AG‑ATCGGAAGAGCacacg                                                           >  1:3552143/1‑96 (MQ=255)       ggTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTTGAG‑ATCGGAAGAGCacacgt                                                          >  1:123779/1‑95 (MQ=255)       ggTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTA‑G‑‑ATCGGAAGAGCacacgtct                                                        >  1:3221204/1‑93 (MQ=255)       ggTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGAT‑AG‑ATCGGAAGAGCacacgtc                                                         >  1:531826/1‑94 (MQ=255)       ggTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGGCAACATGTT‑A‑‑ATCGGAAGCGCATCGGCTa                                                        >  1:1395023/1‑100 (MQ=255)         tGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTT‑AG‑ATCGGAAGAGCacacgtctg                                                       >  1:1146510/1‑92 (MQ=255)         tGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTT‑AAGATCGGAAGAGCacacgtct                                                        >  1:1590013/1‑93 (MQ=255)          gCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTA‑G‑‑ATCGGAAGAGCacacgtctgaa                                                     >  1:5518692/1‑90 (MQ=255)          gCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGAA‑AG‑ATCGGAAGAGCAACGTCTgaa                                                      >  1:4162804/1‑100 (MQ=255)          gCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACAGGTT‑AG‑ATCGGAAGAGCacacgtctga                                                      >  1:3364741/1‑91 (MQ=255)          gCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAAC‑TGTT‑AG‑ATCGGAAGAGCacacgtctgaa                                                     >  1:4243009/1‑90 (MQ=255)                                                ccTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTT‑A‑‑ATCGGAAGCGCATCGGCTAAATGGGGTATTTTAGGACCGATATTCGTACCAATGTTAATc               >  1:3495184/2‑100 (MQ=255)                                                             gTACTGAGTGCAATGGTCAACATGTT‑A‑‑ATCGGAAGCGCATCGGCTAAATGGGGTATTTTAGGACCGATATTCGTACCAATGTTAATCCTTATCGGCtttg  <  1:2939868/100‑2 (MQ=255)                                                                                                   |                                                                 GTTAAAGGTGCCAAATTATTAGAACATCAAAACGGTATTGTATTGATACTAGGTATTATTGTACTGAGTGCAATGGTCAACATGTT‑A‑‑ATCGGAAGCGCATCGGCTAAATGGGGTATTTTAGGACCGATATTCGTACCAATGTTAATCCTTATCGGCTTTC  >  NC_007793/2604112‑2604271

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑