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%	84.9 / NA	24	D388Y (GAT→TAT)	fpgS	Folylpolyglutamate synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (13/11);  total (13/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCTTCATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGGTTT  >  USA300TCH1516_ALE/1761752‑1762024                                                                                                                                          |                                                                                                                                        ttcttcATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATatac                                                                                                                                      >  1:372123/1‑141 (MQ=255)                   gttttagttttaTAAAGCTTCAAAGTACAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCAtt                                                                                                                    <  1:264279/141‑1 (MQ=255)                      ttagttttaTAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAGTTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTc                                                                                                                 >  1:161050/1‑141 (MQ=255)                             tataATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAAtacta                                                                                                          >  1:393856/1‑141 (MQ=255)                                      tCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAAtt                                                                                                 >  1:121878/1‑141 (MQ=255)                                       cAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAAttt                                                                                                >  1:401372/1‑141 (MQ=255)                                            tCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTtcttct                                                                                           >  1:432058/1‑141 (MQ=255)                                                  tttGATTTAACTTCACTTATGAAATAGAGACTTCCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGt                                                                                     <  1:423864/141‑1 (MQ=255)                                                  tttGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGt                                                                                     <  1:417988/141‑1 (MQ=255)                                                   ttGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACATAGGCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTa                                                                                    <  1:160790/141‑1 (MQ=255)                                                              tCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCGTTTTCAATACTACCTACCATTTCTTTTTTGCGTAAAGCTTTCGGa                                                                         >  1:54789/1‑141 (MQ=255)                                                                   tATTAAATACCGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATc                                                                    <  1:43031/141‑1 (MQ=255)                                                                   tATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAAta                                                                    >  1:101201/1‑140 (MQ=255)                                                                      taaaTACAGACCACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCaaa                                                                 <  1:115109/140‑1 (MQ=255)                                                                            cAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGt                                                           <  1:134915/141‑1 (MQ=255)                                                                              gACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTg                                                         >  1:35991/1‑141 (MQ=255)                                                                                 tACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCAt                                                      <  1:454991/141‑1 (MQ=255)                                                                                 tACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCAt                                                      <  1:455015/141‑1 (MQ=255)                                                                                  aCCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATa                                                     <  1:68936/141‑1 (MQ=255)                                                                                    cGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATaaa                                                   >  1:247554/1‑141 (MQ=255)                                                                                            aCTAATGTATCACCTTGATAATTTTTTATAAAGTCAACGTAGTCATATACTAATTGCATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATgc                                           >  1:128972/1‑141 (MQ=255)                                                                                             cTAATGTATCACCTTGAGAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGTGTTTCAAATTCAGTTGCATAAAACGTATgcg                                          <  1:18005/141‑1 (MQ=255)                                                                                                          ttGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAACCTTaa                             >  1:151557/1‑141 (MQ=255)                                                                                                                                     gTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGGttt  >  1:370112/1‑141 (MQ=255)                                                                                                                                     gTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCATTAATCGGttt  >  1:370164/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                        TTCTTCATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGGTTT  >  USA300TCH1516_ALE/1761752‑1762024

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: ‑