Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	2,086,585	C→A	intergenic (‑374/‑311)	SAUSA300_RS10525 ← / → SAUSA300_RS10530	hypothetical protein/chemotaxis inhibitory protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,086,585	0	C	A	87.5%	14.0 / ‑2.8	8	intergenic (‑374/‑311)	SAUSA300_RS10525/SAUSA300_RS10530	hypothetical protein/chemotaxis inhibitory protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (4/3);  minor base . (1/0);  total (5/3)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.65e-01

TTGAAAACGCCCAAGGTAATATTAACATAAAATGGCTACTATTGCATTATCTAATTTTATTTAATTAAAACAAATATATATAGCACAAAAAAACTAGCCCGAAGGCTAGCTTATGAATAGATGAAAATTTGAACACATTGCTGTGTCTAAGATAAATATAGCAC  >  NC_007793/2086500‑2086663                                                                                      |                                                                               ctGAAAACGCCCAAGGTAATATTAACATAAAATGGCTACTATTGCATTATCTAATTTTATTTAATTAAAACAA‑‑ATATATAGCAAAAAAAAACTAGCCCGa                                                                >  1:1991629/2‑100 (MQ=255)  tGAAAACGCCCAAGGTAATATTAACATAAAATGGCTACTATTGCATTATCTAATTTTATTTAATTAAAACAA‑‑ATATATAGCAAAAAAAAACTAGCCAGat                                                               >  1:5507787/1‑99 (MQ=255)      aaCGCCCAAGGTAATATTAACATAAAATGGCTACTATTGCATTATCTAATTTTATTTAATTAAAACAA‑‑ATATATAGCAAAAAAAAACTAGCCCGAAgatc                                                           >  1:4762965/1‑97 (MQ=255)         acccAAGGTAATATTAACATAAAATGGCTACTATTGCATTATCTAATTTTATTTAATTAAAACAA‑‑ATATATAGCAAAAAAAAACTAGCCCGAAgatcgga                                                        >  1:4632037/2‑94 (MQ=255)           ccAAGGTAATATTAACATAAAATGGCTACTATTGCATTATCTAATTTTATTTAATTAAAACAA‑‑ATATATAGCA‑AAAAAAACTAGCCCGAAGGCTAGCTTa                                                     >  1:3887596/1‑100 (MQ=255)                                             cgttATCTAATTTTATTTAATTAAAACAA‑‑ATATATAGCAAAAAAAAACTAGCCCGAAGGCTAGCTTATGAATAGATGAAAATTTGAACACATTGCtgtgg                    <  1:1109673/98‑2 (MQ=25)                                                  tCTAATTTTATTTAATTAAAACAA‑‑ATATATAGCAAAAAAAAACTAGCCCGAAGGCTAGCTTATGAATAGATGAAAATTTGAACACATTGCTGTGTCtgcg               <  1:2686236/100‑4 (MQ=25)                                                               aattaaAACAA‑‑ATATATAGCAAAAAAAAACTAGCCCGAAGGCTAGCTTATGAATAGATGAAAATTTGAACACATTGTTGTGTCTAAGATAAATATAGcag  <  1:4279133/100‑2 (MQ=21)                                                                                      |                                                                               TTGAAAACGCCCAAGGTAATATTAACATAAAATGGCTACTATTGCATTATCTAATTTTATTTAATTAAAACAAATATATATAGCACAAAAAAACTAGCCCGAAGGCTAGCTTATGAATAGATGAAAATTTGAACACATTGCTGTGTCTAAGATAAATATAGCAC  >  NC_007793/2086500‑2086663

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑