Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	1,336	+A	intergenic (+340/‑243)	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	1,334	1	.	A	81.8%	56.8 / 6.4	22	intergenic (+338/‑245)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base . (4/0);  new base A (2/16);  total (6/16)
Fisher's exact test for biased strand distribution p-value = 2.05e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

ATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTT‑AATTTGCATGTAAATGGGCAGTGT‑TAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTC  >  NC_007790/1254‑1424                                                                                  |                                                                                            tgtcttGATTTTTGAT‑AAAAACGCCCTACAGGAATTTAGAAAAACGTGGGGAAGTTTTAAAGAATTTTATGCTAATTTTT‑AATTTGCATGTAAATGGGCa                                                                         >  1:3865188/3‑100 (MQ=255)  ttctaagtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGc                                                                          <  1:1058667/93‑1 (MQ=255)  ttctaagtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGc                                                                          <  1:5884527/93‑1 (MQ=255)  ttctaagtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGc                                                                          <  1:3773216/93‑1 (MQ=255)   ccttgATTTTTGAT‑AAAAACGCCCTACAGGAATTTAGAAAAACGTGGGGAAGTTTTAAAGAATTTTATGCTAATTTTT‑AATTTGCATGTAAAGGGGCAga                                                                       >  1:63999/5‑99 (MQ=255)     taagtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAgt                                                                       <  1:5951224/96‑1 (MQ=255)     taagtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAgt                                                                       <  1:3292936/96‑1 (MQ=255)     taagtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAgt                                                                       <  1:5848628/96‑1 (MQ=255)     taagtttttGATAAGAAAAGCCCGGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAgt                                                                       <  1:3021174/96‑1 (MQ=255)     taagttttaGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAgt                                                                       <  1:4753754/96‑1 (MQ=255)      tgATTTTTGAT‑AAAAACGCCCTACAGGAATTTAGAAAAACGTGGGGAAGTTTTAAAGAATTTTATGCTAATTTTT‑AATTTGCATGTAAATggtgcagatc                                                                    >  1:4254038/2‑92 (MQ=255)      aagtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAgta                                                                      <  1:3324491/97‑2 (MQ=255)       agtttttGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAgtat                                                                     <  1:2243612/98‑3 (MQ=255)                         cccTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTg                                                   <  1:4204140/100‑1 (MQ=255)                                  aaTTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTGATTTTGCTg                                          <  1:2406676/100‑1 (MQ=255)                                            aaCGTGGGGAAGTTTTAAAGAATTTTATGCTAATTTTT‑AATTTGCATGTAAATGGGCAGTGT‑CTAAAAA‑TAGTTATTGTTTTTGCTCAAATTtttgtttt                             >  1:2588190/1‑99 (MQ=255)                                              acaggggAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTGATTTTGCTGAAATTtttgttt                              >  1:2289694/6‑100 (MQ=255)                                               ccggggAAGTTTTAAAGTATTTTATGCTAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTGATTTTGCTGAAATTtttgtttg                             >  1:5939659/5‑100 (MQ=255)                                                                        gCTAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGc    <  1:3617246/100‑1 (MQ=255)                                                                         cTAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCt   <  1:3639112/100‑1 (MQ=255)                                                                          tAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCtg  <  1:3861449/100‑2 (MQ=255)                                                                          tAATTTTTAAATTTGCATGTAAATGGGCAGTATCTAAAAAATTAGTCACTGATTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATTTATTTGGCTc  <  1:4484414/100‑1 (MQ=255)                                                                                  |                                                                                            ATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTT‑AATTTGCATGTAAATGGGCAGTGT‑TAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTC  >  NC_007790/1254‑1424

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑