Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,362	G→A	100%	H104Y (CAC→TAC)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,362	0	G	A	100.0%	94.3 / NA	33	H104Y (CAC→TAC)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (16/17);  total (16/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCC  >  USA300TCH1516_ALE/1744229‑1744497                                                                                                                                        |                                                                                                                                        attATAAATCCAATACCAACAACGATACCGCCTAACGTTTCAACTAATTTTAATGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCAGCGGTAACTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGt                                                                                                                                   <  1:351020/140‑1 (MQ=255)  ttATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCACTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TTACCTGGTTTAATTGCATCT‑TTGTACATTGtt                                                                                                                                  >  1:202228/1‑140 (MQ=255)  ttATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTTGTTTAATTGCATCT‑TTGTACATTGtt                                                                                                                                  >  1:231547/1‑140 (MQ=255)           cAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACAttt                                                                                                                         <  1:112962/140‑1 (MQ=255)             aTACCTACTTCGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAACTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGt                                                                                                                       <  1:496997/140‑1 (MQ=255)                ccTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTAcc                                                                                                                    <  1:477933/140‑1 (MQ=255)                    ctacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCATCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAGAACATTTGTACCatat                                                                                                                <  1:428356/140‑1 (MQ=255)                      acGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTc                                                                                                              <  1:277846/140‑1 (MQ=255)                         aTACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAg                                                                                                           <  1:279100/140‑1 (MQ=255)                            ccGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTc                                                                                                        >  1:238883/1‑140 (MQ=255)                             cGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                       >  1:736367/1‑140 (MQ=255)                               ccTAATTTTTCAACTAGTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATa                                                                                                     >  1:392998/1‑140 (MQ=255)                                      tttCAACTAACTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATaa                                                                                              >  1:248925/1‑140 (MQ=255)                                                    aTTGCTGCTTCAATCGTACCACCAGAAGCTAATAAATCATCTGTGATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACg                                                                                >  1:419299/1‑140 (MQ=255)                                                      tgctgcTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATAT‑TTGTACATTTTTAAAACATTTGTACCATATTCTAGGTCATAATAATAACGAATGACTTCACGAg                                                                              >  1:155774/1‑140 (MQ=255)                                                       gctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACATGGCTTAATGGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAgg                                                                             <  1:364537/140‑1 (MQ=255)                                                                   gTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCcttc                                                                 <  1:415941/140‑1 (MQ=255)                                                                       caccaGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCtttt                                                             <  1:6560/140‑1 (MQ=255)                                                                          catgaGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTa                                                          <  1:357829/136‑1 (MQ=255)                                                                          caGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTa                                                          >  1:537829/1‑140 (MQ=255)                                                                              aGCTAATAAATCATCTGTAATTCA‑TCGCGTATTACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTCACAg                                                      >  1:182193/1‑140 (MQ=255)                                                                                 taataaATCATCTGTAATTAACACACGC‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTg                                                   <  1:530787/140‑1 (MQ=255)                                                                                   ataaATCATCTGTAATTAATAAACGT‑TTACCTTTTTTCTTTG‑ACCTGATGCACAGTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCa                                                 <  1:748636/140‑1 (MQ=255)                                                                                      aaTCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGATCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAg                                              >  1:643104/1‑140 (MQ=255)                                                                                         catcTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGCGCAAAGCCa                                           <  1:561614/140‑1 (MQ=255)                                                                                           tcTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGTTGCAAACCCAAt                                         >  1:705476/1‑140 (MQ=255)                                                                                             tGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGAACTTTCCCTTCTTTTCTACAAGGTGCGAAGCCAATcc                                       >  1:629208/1‑140 (MQ=255)                                                                                              gTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATccc                                      >  1:150026/1‑140 (MQ=255)                                                                                                aaTTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                    <  1:538174/140‑1 (MQ=255)                                                                                                    aaCACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGa                                >  1:265426/1‑140 (MQ=255)                                                                                                          cGT‑TGACCTGGTTTAATTGCATCT‑TTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                          <  1:391728/140‑1 (MQ=255)                                                                                                                             gCATCT‑TTGTACATTGTTAAAACATTTGTTCCATATTCTAGGTCTTACTCTTAACGATTGTCTTCACGTTGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGAt        <  1:204311/140‑1 (MQ=255)                                                                                                                                    ttGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGAACAGCCAATGATAAAGcc  >  1:382862/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        ATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGT‑TGACCTGGTTTAATTGCATCT‑TTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCC  >  USA300TCH1516_ALE/1744229‑1744497

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑