Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	607,884	G→A	100%	R209* (CGA→TGA)	dck ←	Deoxyadenosine/deoxycytidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	607,884	0	G	A	100.0%	144.8 / NA	45	R209* (CGA→TGA)	dck	Deoxyadenosine/deoxycytidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/16);  total (29/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAG  >  USA300TCH1516_ALE/607752‑608020                                                                                                                                     |                                                                                                                                         gtgAATTATTGTATTCGATTGAATTGATAATATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAtt                                                                                                                                   <  1:279614/140‑1 (MQ=255) gtgAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAtt                                                                                                                                   <  1:458593/140‑1 (MQ=255)          tGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                          >  1:372917/1‑140 (MQ=255)            tATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTATACTTTTATAATGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTtattat                                                                                                                        >  1:20684/1‑140 (MQ=255)             aTTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACTTATATGCTAAGTCGTAAGACTTTTAACGAGTATCGACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATa                                                                                                                       >  1:725013/1‑140 (MQ=255)             aTTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTATTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATa                                                                                                                       >  1:30086/1‑140 (MQ=255)                  aTAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACTTTTTAGCCAAGACCTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAtt                                                                                                                  <  1:176517/140‑1 (MQ=255)                     gAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTaa                                                                                                               <  1:606729/140‑1 (MQ=255)                     gAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTaa                                                                                                               <  1:706918/140‑1 (MQ=255)                       aTTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTTTATCTACTTGTCGATATATTTGAATAATTCAAGCAATTTTGTTAATCAAAGGACTTAAAg                                                                                                             >  1:286863/1‑140 (MQ=255)                       aTTGATAAAATAATCGATAAGATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCGATTTTGTTTATCATAGGATTTAAAg                                                                                                             >  1:463784/1‑140 (MQ=255)                                 taatCGAT‑ATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTcc                                                                                                  <  1:581285/140‑1 (MQ=255)                                  aatCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTCTCTCTTTATTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTcc                                                                                                  <  1:553858/140‑1 (MQ=255)                                    tCGATAATATCAATGTAATATACATTGAATATAAACATATTCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCtt                                                                                                <  1:97222/140‑1 (MQ=255)                                     cGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTa                                                                                               >  1:340780/1‑140 (MQ=255)                                         aataTCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACATGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCAGGGTCCTTATGGa                                                                                           >  1:217289/1‑140 (MQ=255)                                               tagggAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTATTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCat                                                                                     <  1:23840/137‑1 (MQ=255)                                                       ataCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTa                                                                             >  1:635258/1‑140 (MQ=255)                                                       ataCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGAGGTCCTTATGGATATCATATTCAtaa                                                                             >  1:246887/1‑138 (MQ=255)                                                         aCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTTTGGTTATCATATTCATTAat                                                                           >  1:120011/1‑140 (MQ=255)                                                               aaTATAAACATATACGCTATGTCTTCAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATCTCATATTCATTAATATTGAt                                                                     <  1:467435/140‑1 (MQ=255)                                                                atatAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGTGTCCTTATGAATATCATATTCATTAATATTGATa                                                                    >  1:189745/1‑140 (MQ=255)                                                                     aaCATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTAc                                                               >  1:72357/1‑140 (MQ=255)                                                                     aaCATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTGGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTAc                                                               >  1:509421/1‑140 (MQ=255)                                                                     aaCATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGAAATGGTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTAc                                                               >  1:146663/1‑140 (MQ=255)                                                                      aCATATAAGCTATGTCTTTAGTCTTTTATCGTGTAACTATTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACa                                                              <  1:486828/140‑1 (MQ=255)                                                                       cATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACaa                                                             >  1:605892/1‑140 (MQ=255)                                                                            aCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCTATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGa                                                        <  1:45981/140‑1 (MQ=255)                                                                            aCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTgaa                                                        >  1:99763/1‑138 (MQ=255)                                                                            aCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGa                                                        >  1:165704/1‑140 (MQ=255)                                                                             cGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGAc                                                       >  1:603382/1‑140 (MQ=255)                                                                                   gTCTTTAGTCTTTTATCGTGAATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCAt                                                 >  1:537541/1‑140 (MQ=255)                                                                                       ttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACCAGCATTaaa                                             >  1:185345/1‑140 (MQ=255)                                                                                         aGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTATAGc                                           >  1:315975/1‑140 (MQ=255)                                                                                                tATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGATATTAAt                                    >  1:493587/1‑140 (MQ=255)                                                                                                           tACTTGTCGATATGTTTGAATAATTCAAGAAATGTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCAt                         >  1:369232/1‑140 (MQ=255)                                                                                                            aCTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATa                        >  1:268662/1‑140 (MQ=255)                                                                                                            aCTTGTCGATATGTTTCAATATTTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATa                        >  1:393248/1‑140 (MQ=255)                                                                                                               tGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCg                     <  1:574878/140‑1 (MQ=255)                                                                                                                      atttttGAACAATTCAAGCAATTTTGTTTATCAGAGCATTTAAAGATTCGGTGTCCTTATGGATATCATATTCATTAATATTAATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAAt              <  1:49004/137‑1 (MQ=255)                                                                                                                      atGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAAt              <  1:270376/140‑1 (MQ=255)                                                                                                                          ttGAATAATTCAAGTAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCt          <  1:246124/140‑1 (MQ=255)                                                                                                                           tGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCtt         >  1:59125/1‑140 (MQ=255)                                                                                                                                 atTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCa   >  1:389137/1‑140 (MQ=255)                                                                                                                                  ttCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCAATTAATCCAATCGTCATACCGTTTAAATAGCTTTTTCCAg  >  1:499826/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                                         GTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCAG  >  USA300TCH1516_ALE/607752‑608020

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: ‑