Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,627,280	(AT)5→6	intergenic (‑215/‑107)	sarT ← / → sarU	staphylococcal accessory regulator T/staphylococcal accessory regulator U

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,627,269	1	.	T	94.4%	56.1 / ‑2.1	18	intergenic (‑204/‑118)	sarT/sarU	staphylococcal accessory regulator T/staphylococcal accessory regulator U
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base T (7/10);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01
*	CP000730	2,627,269	2	.	A	94.4%	55.5 / ‑2.0	18	intergenic (‑204/‑118)	sarT/sarU	staphylococcal accessory regulator T/staphylococcal accessory regulator U
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base A (7/10);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

ATAACTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑TATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAG  >  CP000730/2627122‑2627410                                                                                                                                                     ||                                                                                                                                              ataaCTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATGGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTAtttatattt                                                                                                                                                 >  1:233087/1‑148 (MQ=255)        cAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑tatatat                                                                                                                                        <  1:58478/148‑1 (MQ=255)             atatTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑Tatatatatata                                                                                                                                   <  2:361826/148‑2 (MQ=255)                             tctagctaTAAACACATATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATAtt                                                                                                                     <  2:318717/147‑1 (MQ=255)                                 gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg                                                                                                                 >  1:354458/1‑148 (MQ=255)                                 gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg                                                                                                                 >  1:125275/1‑148 (MQ=255)                                 gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg                                                                                                                 <  2:123757/148‑1 (MQ=255)                                  ctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGt                                                                                                                >  1:172055/1‑148 (MQ=255)                                             aaTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCtt                                                                                                     <  1:152978/148‑1 (MQ=255)                                             aaTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCtt                                                                                                     >  1:306936/1‑148 (MQ=255)                                              aTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCttt                                                                                                    >  2:354769/1‑148 (MQ=255)                                                                                 tGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTATGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTTaatatttt                                                                 >  2:384513/1‑144 (MQ=255)                                                                                               gATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACa                                                   <  1:87222/148‑1 (MQ=255)                                                                                                       aTGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGaaaa                                           <  2:172055/148‑1 (MQ=255)                                                                                                          aaTTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAAtag                                        <  1:361464/148‑1 (MQ=255)                                                                                                          aaTTTGTCATTTGTTATTATGTGATTTTTAGTTATTTATATTTTATATATATATATTCTATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAAtag                                        <  1:202123/148‑1 (MQ=255)                                                                                                                        tATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAg                          >  1:13908/1‑148 (MQ=255)                                                                                                                                     ttAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCaaa             <  1:108088/148‑1 (MQ=255)                                                                                                                                     ttAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCaaa             <  1:338454/148‑1 (MQ=255)                                                                                                                                           ttatatttta‑‑tatatATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGaa     <  2:270985/145‑1 (MQ=255)                                                                                                                                           atttatATTTTATATATATATATTATATATAAAATATTTAGTTTAACATGTATTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCg       <  2:22230/148‑1 (MQ=255)                                                                                                                                              tatttta‑‑tatatATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAg  <  1:23152/148‑1 (MQ=255)                                                                                                                                                     ||                                                                                                                                              ATAACTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑TATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAG  >  CP000730/2627122‑2627410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑