Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	222,846	C→A	21.0%	G143V (GGG→GTG)	ptsG_1 ←	PTS system glucose‑specific EIICBA component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	222,846	0	C	A	21.0%	42.9 / 5.7	19	G143V (GGG→GTG)	ptsG_1	PTS system glucose‑specific EIICBA component
Reads supporting (aligned to +/- strand):  ref base C (5/10);  new base A (2/2);  total (7/12)
Fisher's exact test for biased strand distribution p-value = 6.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.96e-01

TGCCATTGGGAATGCTAAAATAAATGATGTTGTAGCCATCATAATAGGTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCATTGTTTTGTTCATGATTATGTA  >  USA300TCH1516_ALE/222713‑222982                                                                                                                                      |                                                                                                                                         tGCCATTGGGAATGCTAAAATAAATGATGTTGTAGCCATCATAATAGGTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATtat                                                                                                                                   <  2:26173/141‑1 (MQ=255)                                gtAGCCATCATAATAGGTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGtt                                                                                                    <  2:63523/141‑1 (MQ=255)                                gtAGCCATCATAATAGGTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGtt                                                                                                    <  2:38985/141‑1 (MQ=255)                                           aataGGTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAGCTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTaa                                                                                         <  1:18190/141‑1 (MQ=255)                                           aataGGTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTaa                                                                                         <  2:66681/141‑1 (MQ=255)                                                          cTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAAcc                                                                          >  1:120861/1‑141 (MQ=255)                                                          cTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAAcc                                                                          >  1:88283/1‑141 (MQ=255)                                                                                     tGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAgg                                               <  1:58117/141‑1 (MQ=255)                                                                                              aaTGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCACGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGgtg                                             >  1:19233/1‑134 (MQ=255)                                                                                              aaTGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCACGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGgtg                                             >  1:19250/1‑134 (MQ=255)                                                                                              aaTGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCACGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGgtg                                             <  2:19250/134‑1 (MQ=255)                                                                                              aaTGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCACGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGgtg                                             <  2:19233/134‑1 (MQ=255)                                                                                                 gTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTaa                                   <  1:11621/141‑1 (MQ=255)                                                                                                             gTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCAt                       >  2:117385/1‑141 (MQ=255)                                                                                                             gTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCAt                       >  2:117364/1‑141 (MQ=255)                                                                                                             gTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCAt                       <  1:95653/141‑1 (MQ=255)                                                                                                                  aaCACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCAttgttt                  <  1:66806/141‑1 (MQ=255)                                                                                                                                aGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCATTGTTTTGTTCATGATTATg    <  1:101200/141‑1 (MQ=255)                                                                                                                                  ggCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCATTGTTTTGTTCATGATTATGTa  >  2:3678/1‑141 (MQ=255)                                                                                                                                      |                                                                                                                                         TGCCATTGGGAATGCTAAAATAAATGATGTTGTAGCCATCATAATAGGTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACTTGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTAATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATATTCTTAGGTGTAACTTGTAAAAAGTCGCCCATTGTTTTGTTCATGATTATGTA  >  USA300TCH1516_ALE/222713‑222982

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑