Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	1,280	C→T	intergenic (+284/‑299)	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	1,280	0	C	T	90.5%	44.7 / ‑4.5	21	intergenic (+284/‑299)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base T (6/13);  total (8/13)
Fisher's exact test for biased strand distribution p-value = 1.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTGTTAAAAAATTAGTCAC  >  NC_007790/1220‑1373                                                             |                                                                                                acgtagttACGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGAt                                                        >  1:4691524/7‑100 (MQ=255)   gtagttACGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGCAGTTTTACAGGAttt                                                      >  1:647344/5‑100 (MQ=255)     agttACGGAGTTCTTAGAGAAAAAATAAAACTTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTa                                                    >  1:5871432/3‑100 (MQ=255)      gttgcGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTAt                                                   >  1:1958292/5‑100 (MQ=255)        tACAGAGTTCTTAGAGATAAATTAAAAATTCTCGATTTTTGATAAAAACCGCTCTGCAGGAATTTAGAAAAACA‑C‑GGGAAAGTTTTAAAGGATTTTATGc                                                 >  1:4018663/1‑100 (MQ=255)        caCGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGc                                                 >  1:4617800/2‑100 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                      <  1:3865303/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                      <  1:5725020/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                      <  1:5422463/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                      <  1:4980665/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc                      <  1:3226450/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAACGGGc                      <  1:2249750/100‑1 (MQ=255)                                   attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCAGGGAAATGGGc                      <  1:1760247/100‑1 (MQ=255)                                    ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCa                     <  1:1630375/100‑1 (MQ=255)                                    ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCa                     <  1:2036675/100‑1 (MQ=255)                                        tcgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgtg                  <  1:3352581/96‑1 (MQ=255)                                        tcgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAAGGGGCAgat                  <  1:3152989/96‑3 (MQ=255)                                         cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAATGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgtgg                 <  1:4507874/97‑2 (MQ=255)                                         cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACA‑TGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgcag                 >  1:3220985/4‑97 (MQ=255)                                                   aaaaaaTGTCTTGCAGGAATTTAGAAAAACAGG‑GGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAGTGTTtaaaaaaat       <  1:5734429/100‑4 (MQ=255)                                                      aaaCGCTCTGCAGGAATTTAGAAAAACA‑C‑GGGAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTGTTACAAAA‑TAGTCat  >  1:2282828/1‑99 (MQ=255)                                                             |                                                                                                ATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACA‑T‑GTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTGTTAAAAAATTAGTCAC  >  NC_007790/1220‑1373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑