Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,761,889	C→A	100%	D388Y (GAT→TAT)	fpgS ←	Folylpolyglutamate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,761,889	0	C	A	100.0%	61.9 / NA	21	D388Y (GAT→TAT)	fpgS	Folylpolyglutamate synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (14/7);  total (14/7)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGG  >  USA300TCH1516_ALE/1761759‑1762021                                                                                                                                   |                                                                                                                                     tGGCTATTTTAGTTTTAGTTTTATAATGCTTCCAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATACCCTTGATAATTTTTTATAAATTCAACCTAGTCATATAATAAttct                                                                                                                            >  2:96771/1‑139 (MQ=255)  ggCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTa                                                                                                                           >  2:323998/1‑141 (MQ=255)   gCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTAt                                                                                                                          >  1:313879/1‑141 (MQ=255)            gttttagttttaTAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTCTTTCATCAtt                                                                                                                 >  1:370435/1‑141 (MQ=255)                        taATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCCCATTTTTCAAgactaac                                                                                                     <  2:183957/141‑3 (MQ=255)                        aaaTGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActacc                                                                                                     <  1:102662/140‑1 (MQ=255)                            gCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACa                                                                                                 >  1:318903/1‑141 (MQ=255)                            gCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACa                                                                                                 >  2:150967/1‑141 (MQ=255)                             cTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTGATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACaa                                                                                                <  1:242261/141‑1 (MQ=255)                                  aaGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAAtttat                                                                                           >  1:53632/1‑139 (MQ=255)                                     tCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCTTTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTtcttct                                                                                        >  2:392044/1‑141 (MQ=255)                                          ttttGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTCGTCTTATACTAATTGTATTTCATCATACTCAATGCTACCTACAATATCATCTTTGCg                                                                                   >  1:325263/1‑141 (MQ=255)                                                tttAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCATGATAGTTTTTTATAAATTCAACGTAAGCAGATACTAAATGTATTTCATCAATTTCAACACTACCTACAATTACTTCTTTTAGGAACGc                                                                             >  2:190719/1‑141 (MQ=255)                                                                        aCTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGc                                                     >  1:121027/1‑141 (MQ=255)                                                                              ggTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATaaaa                                               <  2:371898/141‑1 (MQ=255)                                                                                              tCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTaaa                               >  2:205222/1‑141 (MQ=255)                                                                                                   ttGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTaa                          <  1:351226/141‑1 (MQ=255)                                                                                                        aaTTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGtt                     >  2:268404/1‑141 (MQ=255)                                                                                                                    aTTCAACGTAGTCATATACTAATTTTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGt         <  2:313879/141‑1 (MQ=255)                                                                                                                    aTTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGt         <  1:234047/141‑1 (MQ=255)                                                                                                                           gTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCgg  >  2:139462/1‑141 (MQ=255)                                                                                                                                   |                                                                                                                                     TGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGG  >  USA300TCH1516_ALE/1761759‑1762021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑