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%	101.2 / 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.

TGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCA  >  USA300TCH1516_ALE/1744237‑1744498                                                                                                                              |                                                                                                                                         tGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACAtt                                                                                                                           >  1:346138/1‑141 (MQ=255) tGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACAtt                                                                                                                           >  1:325989/1‑141 (MQ=255)       aCCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTccc                                                                                                                     >  1:473100/1‑141 (MQ=255)                    ccGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                        <  1:393141/141‑1 (MQ=255)                    ccGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGAACCATATTCTAGGTCa                                                                                                        <  1:377907/141‑1 (MQ=255)                         tAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCCGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTc                                                                                                   <  1:517719/141‑1 (MQ=255)                         tAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTTTACCATATTCTAGGTCATACTc                                                                                                   >  1:278526/1‑141 (MQ=255)                         tAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTc                                                                                                   <  1:603405/141‑1 (MQ=255)                         tAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTc                                                                                                   <  1:97018/141‑1 (MQ=255)                             ttttCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATaa                                                                                               <  1:63392/141‑1 (MQ=255)                                    cTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGa                                                                                        >  1:299122/1‑141 (MQ=255)                                            aTTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTAAATTGCATCTTTGTATGTCGCTAACGGGTTTGGACATGATTCTATGTCATAATCATAACGAATTACttaagga                                                                                >  1:359376/1‑136 (MQ=255)                                                    ttCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATTCTCATAACGAATGACTTCACGAGGTAAttt                                                                        <  1:760212/141‑1 (MQ=255)                                                     tCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTc                                                                       <  1:693788/141‑1 (MQ=255)                                                            tACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTCGGTCCTACTCATAACGTATGACTTCACGAGGTAATTTCCcttctt                                                                >  1:327244/1‑141 (MQ=255)                                                            tACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACATGGATTCCCTGCATCTTTACAAAAAGAAAAAACATTTGTACCATATTCTAGGACATACTCGTAACGAAGGACTGCACGAGGTGATTTCCctgctt                                                                >  1:756363/1‑141 (MQ=255)                                                               caccaGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTc                                                             <  1:127624/141‑1 (MQ=255)                                                                    gTAGCTAATAAATCATCTGAAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCTTACTCATAACGAATGACTTCACGAGGTAGTTTTCCTTCTTTTCTAACa                                                        >  1:405370/1‑141 (MQ=255)                                                                     tAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAg                                                       >  1:729129/1‑141 (MQ=255)                                                                        cTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATATTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTGCACGAGGTAATTTCCCTTTTTTTCTAACAGGTg                                                    >  1:1358/1‑141 (MQ=255)                                                                             aaaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATCACGCATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAg                                               <  1:524760/141‑1 (MQ=255)                                                                                       tAATTAACACCCGTTGCCCTGGTTTAATTGCATCTTTGTACATTGGTAAAACATTTGTACCATATTCTAGGTCATTCTCATAACGGACGACTTCAAAAAAGCGTGCCCTTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                     <  1:757007/141‑1 (MQ=255)                                                                                        aaTTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCAt                                    <  1:214467/141‑1 (MQ=255)                                                                                              cacacGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCCATCCCCATTGAATa                              >  1:106253/1‑141 (MQ=255)                                                                                              cacacGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTTAATa                              >  1:195535/1‑141 (MQ=255)                                                                                                      gACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCACTCCCCACTGAATAAGCTACAg                      <  1:397478/141‑1 (MQ=255)                                                                                                      gACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAg                      <  1:337539/141‑1 (MQ=255)                                                                                                       aCCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAgg                     <  1:482958/141‑1 (MQ=255)                                                                                                             tttAAGTGCATCGTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTCCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGcc               <  1:57496/141‑1 (MQ=255)                                                                                                                aaTTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAAt            >  1:473799/1‑141 (MQ=255)                                                                                                                   tGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGGGGTAATTTCCCTTTTTTTCTGCTTCTTGCAAAGCAAAACAACGTTCAAAGACCTACAGGACAGCCAATGAt         >  1:749300/1‑141 (MQ=255)                                                                                                                     cATCTTTGTACATTGTTAAAACATTTGTACCATGTTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTACCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCCTGGAATAAGCTACAGGACGGCCAATGCTaa       >  1:167032/1‑141 (MQ=255)                                                                                                                          ttGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCa  <  1:549223/141‑1 (MQ=255)                                                                                                                              |                                                                                                                                         TGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCA  >  USA300TCH1516_ALE/1744237‑1744498

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: ‑