Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	1,357	G→A	intergenic (+361/‑222)	SAUSA300_RS14705 → / → SAUSA300_RS14710	replication protein/membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,357	0	G	A	84.0%	49.0 / 1.8	25	intergenic (+361/‑222)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base G (4/0);  new base A (4/17);  total (8/17)
Fisher's exact test for biased strand distribution p-value = 5.53e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01

CCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTT‑AATTTGCATGTAAATGGGCAGT‑GT‑TAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGT  >  NC_007790/1278‑1447                                                                                  |                                                                                            cccTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTg                                                                          <  1:4204140/100‑1 (MQ=255)          aaTTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTg                                                                 <  1:2406676/100‑1 (MQ=255)                    aaCGTGGGGAAGTTTTAAAGAATTTTATGCTAATTTTT‑AATTTGCATGTAAATGGGCAGT‑GT‑CTAAAAA‑TAGTTATTGTTTTTGCTCAAATTtttgtttt                                                    >  1:2588190/1‑99 (MQ=255)                      acaggggAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTtttgttt                                                     >  1:2289694/6‑100 (MQ=255)                       ccggggAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTtttgtttg                                                    >  1:5939659/5‑100 (MQ=255)                                                gCTAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGc                           <  1:3617246/100‑1 (MQ=255)                                                 cTAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCt                          <  1:3639112/100‑1 (MQ=255)                                                  tAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCtg                         <  1:3861449/100‑2 (MQ=255)                                                  tAATTTTTAAATTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTc                         <  1:4484414/100‑1 (MQ=255)                                                        ttaaaTTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATAtta                   <  1:5619554/97‑2 (MQ=255)                                                           aaTTTGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCg                <  1:4073232/100‑1 (MQ=255)                                                             tttGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCGCTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtt              <  1:1144220/100‑1 (MQ=255)                                                             tttGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtt              <  1:4644747/100‑1 (MQ=255)                                                              cagCATGTAAATGGGCAGT‑GT‑CTAAAAA‑TAGTTATTGTTTTTGCTCAAATTTTTGTTTTTGAAAATAGCATATATTTATTTGGCTCATATTTGCGTTTTa           >  1:2404927/3‑100 (MQ=255)                                                               tGCATGTAAATGGGCAGTATT‑TAAAAAATTAGTCACTGATTTTGTTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtttt            <  1:1420309/100‑1 (MQ=255)                                                               tGCATGTAAATGGGCAGT‑GT‑CTAAAAA‑TAGTTATTGTTTTTGCTCAAATTTTTGTTTTTGAAAATAGCATATATTTATTTGGCTCATATTTGCGTTTTaa          >  1:2720352/1‑100 (MQ=255)                                                               tGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGACATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtttt            <  1:5005935/100‑1 (MQ=255)                                                               tGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtttt            >  1:1253700/1‑100 (MQ=255)                                                               tGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtttt            <  1:4580945/100‑1 (MQ=255)                                                               tGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtttt            >  1:2602478/1‑100 (MQ=255)                                                               tGCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCCGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGtttt            <  1:270719/100‑1 (MQ=255)                                                                gCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGTTTTa           <  1:1104449/100‑1 (MQ=255)                                                                gCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGTTTTa           <  1:4020880/100‑1 (MQ=255)                                                                gCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGTTTTa           <  1:3108343/100‑1 (MQ=255)                                                                gCATGTAAATGGGCAGT‑ATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTCATATTTGCGTTTTa           <  1:2717283/100‑1 (MQ=255)                                                                       caTGGGCAGT‑GT‑CTAAAAA‑TAGTTATTGTTTTTGCTCAAATTTTTGTTTTTGAAAATAGCATATATTTATTTGGCTCATATTTGCGTTTTAAAAGcatat  >  1:5651500/2‑96 (MQ=255)                                                                                  |                                                                                            CCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTT‑AATTTGCATGTAAATGGGCAGT‑GT‑TAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGT  >  NC_007790/1278‑1447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑