Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	646,838	G→A	55.0%	intergenic (+192/‑395)	lipL → / → galK	Octanoyl‑[GcvH]:protein N‑octanoyltransferase/Galactokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	646,838	0	G	A	55.0%	‑2.1 / 22.6	20	intergenic (+192/‑395)	lipL/galK	Octanoyl‑[GcvH]:protein N‑octanoyltransferase/Galactokinase
Reads supporting (aligned to +/- strand):  ref base G (4/5);  new base A (5/6);  total (9/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.32e-01

TCCATAAAAAGCATAAATATGTTATTGACCTAATATTTAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAGTAGTAAATCTATATATTCCAATTATTATTTGTAGTATTATAGTTAGGGTGGAAAATTATAAATTGTAGGGCT  >  USA300TCH1516_ALE/646704‑646974                                                                                                                                       |                                                                                                                                         tCCATAAAAAGCATAAATATGTTATTGACCTAATATTTAAACTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAGTAAGGtata                                                                                                                                    >  1:191703/1‑141 (MQ=255)      aaaaaGCAAAAATATGTTATTGACCTAATATTTAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATaa                                                                                                                               <  1:121776/141‑1 (MQ=255)       aaaaGCATAAATATGTTATTGACCTAATATTTAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAAt                                                                                                                              >  2:274770/1‑141 (MQ=255)       aaaaGCATAAATATGTTATTGACCTAATATTTAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAAt                                                                                                                              <  1:274770/141‑1 (MQ=255)            cATAAATATGTTATTGACCTAATATTTAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAAAATCTGAGATGACGGATTAAATAGATTGAGAATAAGGTATATATAATGCGTa                                                                                                                         >  1:63570/1‑141 (MQ=255)                               taataaTTAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAATGCGTATGACTATGAAAGAAACGAc                                                                                                      <  2:249759/141‑1 (MQ=255)                                      tAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTAt                                                                                               <  1:252907/141‑1 (MQ=255)                                        aaTTGAACAACATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTg                                                                                             <  2:26911/141‑1 (MQ=255)                                                atcatTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTc                                                                                     >  1:141084/1‑141 (MQ=255)                                                    ttaaattaaaAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAAt                                                                                 <  2:186518/141‑1 (MQ=255)                                                           aaaaGTAATGATATGATGGACATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAAAGTTCTAATACTTtag                                                                          <  1:207269/141‑1 (MQ=255)                                                              aGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTtagtag                                                                       <  2:31383/141‑1 (MQ=255)                                                                tAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAgtagta                                                                     <  2:161169/141‑1 (MQ=255)                                                                tAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAgtagta                                                                     <  2:133497/141‑1 (MQ=255)                                                                              aaaTAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAGTAGTAAATCTATATATTcc                                                       >  1:190249/1‑141 (MQ=255)                                                                                                               tACGTATTAAATAGATTGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAGTAGTAAATCTATATATTCCAATTATTATTTGTAGTATTATAGTTAGGGTGGa                      >  2:227241/1‑141 (MQ=255)                                                                                                                     ttAAATAGATTTAGAATAGGGTATATATAATGCGTATGACTATGAAAAAACCGACCTTCTATTGTAATGTTCTAATACTTTATTAGTATATCTATATAGGCCAATTATTATTTGTAGTAATAGAGTTAGGGTGGAAAATta                <  2:219505/141‑1 (MQ=255)                                                                                                                     ttAAATAGAGTGAGAATAGGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGCAATGTTCTAATACTTTAGTAGTAAATCTATATATTCCAATTATTATTTGTAGTATTATAGTTAGGGTGGAAAATta                >  2:276164/1‑141 (MQ=255)                                                                                                                              ttGAGAATAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAGTAGTAAATCTATATATTCCAATTATTATTTGTAGTATTATCGTTAGGGTGGAAAATTATCAATTGTa       >  1:182206/1‑141 (MQ=255)                                                                                                                                   aaTAAGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAGTAGTAAATCTATATATTCCAATTATTATTTGTAGTATTATAGTTAGGGTGGAAAATTATAAATGGTAGGGCt  >  1:11160/1‑141 (MQ=255)                                                                                                                                       |                                                                                                                                         TCCATAAAAAGCATAAATATGTTATTGACCTAATATTTAAATTGAACATCATTAAATTAAAAGTAATGATATGATGGAAATAATAAATTTAATAAGAAAATTTCATGTTTTACGTATTAAATAGATTGAGAATAGGGTATATATAATGCGTATGACTATGAAAGAAACGACCTTCTATTGAAATGTTCTAATACTTTAGTAGTAAATCTATATATTCCAATTATTATTTGTAGTATTATAGTTAGGGTGGAAAATTATAAATTGTAGGGCT  >  USA300TCH1516_ALE/646704‑646974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑