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%	97.2 / NA	33	R209* (CGA→TGA)	dck	Deoxyadenosine/deoxycytidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/16);  total (17/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCA  >  USA300TCH1516_ALE/607746‑608019                                                                                                                                           |                                                                                                                                        gtATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAg                                                                                                                                       >  1:567530/1‑141 (MQ=255)           aTTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTATTCTTTTATCTTGTATCTCCTGGTCGATATGATTGAATCATTCAGGCAAGTTTGtt                                                                                                                             >  1:169350/1‑141 (MQ=255)              aaTGTATTCGATAGAATTGATAAAATAATCGTTAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTAt                                                                                                                          <  1:344234/141‑1 (MQ=255)              aaTGTATTCGATAGAATTGATAAAATAATCGATAATATGTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTATTATCGTGTATCTACTTGTCGATATGTTTGAATTCTTCAAGCAATTTTGTTTAt                                                                                                                          <  1:529799/141‑1 (MQ=255)               aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                         <  1:115995/141‑1 (MQ=255)                      cGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAt                                                                                                                  >  1:654803/1‑141 (MQ=255)                         tAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATCATTCACGCACTACTGTTTATAATAGGATTTa                                                                                                               >  1:571138/1‑141 (MQ=255)                           gAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATACACATCTGCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGGTATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTaaa                                                                                                             >  1:801290/1‑141 (MQ=255)                              ttGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGTATTTAAAGAt                                                                                                          >  1:634210/1‑141 (MQ=255)                              ttGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAggt                                                                                                          >  1:169968/1‑139 (MQ=255)                                gATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTc                                                                                                        <  1:586349/141‑1 (MQ=255)                                          tCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTa                                                                                              <  1:110173/141‑1 (MQ=255)                                                              taCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAat                                                                          >  1:609717/1‑141 (MQ=255)                                                                  ttGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGAGTCCTTATGGATATCATATTCATTAATATTg                                                                      >  1:231782/1‑141 (MQ=255)                                                                    gAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGAt                                                                    >  1:93354/1‑141 (MQ=255)                                                                       tataAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACg                                                                 >  1:697596/1‑141 (MQ=255)                                                                           aaCATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACa                                                             >  1:453902/1‑141 (MQ=255)                                                                                        tGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAATTTGTATATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCAt                                                <  1:799044/141‑1 (MQ=255)                                                                                             ttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAg                                           <  1:134429/141‑1 (MQ=255)                                                                                                     ttATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAAt                                   >  1:213338/1‑141 (MQ=255)                                                                                                       atagtgtATCTACTTGTCGAGATTGTTTAATACTTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATTGATATCATATTCATTAATATTGATACGTACAACTGGACATGCAGTAAAGCTATTAATcc                                 <  1:104726/138‑1 (MQ=255)                                                                                                         cGTGTATCTACTTGTCGATATTTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCaa                               <  1:138655/141‑1 (MQ=255)                                                                                                            gtATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATct                            >  1:428623/1‑140 (MQ=255)                                                                                                            gtATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCg                            >  1:697818/1‑141 (MQ=255)                                                                                                                    ttGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCg                    <  1:205091/141‑1 (MQ=255)                                                                                                                    ttGGCGATATGGTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCg                    <  1:720299/141‑1 (MQ=255)                                                                                                                         gATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGCTTTATAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTTATTCGTTACACTAGACATGCATTAAAGCTATTAATCCAATAGTAGTAACGTTTaa               >  1:162919/1‑141 (MQ=255)                                                                                                                         gATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTaa               >  1:554976/1‑141 (MQ=255)                                                                                                                             tGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAg           <  1:640621/141‑1 (MQ=255)                                                                                                                                     tgatTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTcc   <  1:585406/139‑1 (MQ=255)                                                                                                                                     taatTCAAGCAATTTTGTTTAGCATAGGATTTAAAGATTCGGGGTCCTTAAGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTcc   <  1:176042/141‑1 (MQ=255)                                                                                                                                      aatTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCa  <  1:658587/141‑1 (MQ=255)                                                                                                                                      aatTCAAGCAATTCTGCTCATCATAGGATTTAAAGATACGGGGTCCTGCTAGATATCAGATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCa  <  1:715562/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                        GTATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTCCA  >  USA300TCH1516_ALE/607746‑608019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑