Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	1,276	C→T	intergenic (+280/‑303)	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	1,276	0	C	T	90.0%	44.0 / ‑2.6	20	intergenic (+280/‑303)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (4/14);  total (5/15)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

AGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACAT‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTGTT  >  NC_007790/1206‑1359                                                                       |                                                                                      aGCAAATTCTCCTTATGCTCTTACAGAGTTCTTAGAGATAAATTAAAAATTCTCGATTTTTGATAAAAAACGCTCTGCAGGAATTTAGAAAAACacggga                                                          >  1:4940118/1‑95 (MQ=255)               acgtagttACGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGAt                                          >  1:4750779/7‑100 (MQ=255)                   agttACGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTa                                      >  1:965894/3‑100 (MQ=255)                   agttACGGAGTTCTTAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTa                                      >  1:4687770/3‑100 (MQ=255)                          ccgatcttAGAGAAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTaac                               <  1:3972355/94‑2 (MQ=255)                                     gaAAAAATAAAAATTCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGc                    <  1:1125429/100‑1 (MQ=255)                                                 attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc        <  1:2614021/100‑1 (MQ=255)                                                 attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc        <  1:2614745/100‑1 (MQ=255)                                                 attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc        <  1:392950/100‑1 (MQ=255)                                                 attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc        <  1:4939075/100‑1 (MQ=255)                                                 attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAACGGGc        <  1:4669875/100‑1 (MQ=255)                                                 attCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACAT‑GGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGc        <  1:1894827/100‑1 (MQ=255)                                                  ttCTCGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCa       <  1:3918417/100‑1 (MQ=255)                                                   tctcGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAg      <  1:1439479/100‑1 (MQ=255)                                                    ctcGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgt     <  1:1881587/100‑1 (MQ=255)                                                    ctcGA‑TTTTGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACCTTTAATTTGCATGTAAATGGGCAgt     <  1:2206515/100‑1 (MQ=255)                                                      tcgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgtg    <  1:2228367/96‑1 (MQ=255)                                                       gATTTTTGATAAAAAACGCTCTGCAGGAATTTAGAAAAACAC‑GG‑GAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGACAGTGtt  <  1:1018041/100‑1 (MQ=255)                                                       cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgtgg   <  1:892268/97‑2 (MQ=255)                                                       cgattttGATAAAAAATGTCTTGCAGGAATTTAGAAAAACATGGG‑GGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCATGTAAATGGGCAgatc   >  1:2124412/4‑97 (MQ=255)                                                                       |                                                                                      AGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACAT‑GT‑GGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGCAGTGTT  >  NC_007790/1206‑1359

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: ‑