Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,483,375	G→T	V45F (GTC→TTC)	USA300HOU_RS12790 →	putative HTH‑type transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,483,375	0	G	T	100.0%	55.8 / NA	16	V45F (GTC→TTC)	USA300HOU_RS12790	putative HTH‑type transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (12/4);  total (12/4)

TTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTTTAT  >  USA300TCH1516_ALE/2483257‑2483500                                                                                                                       |                                                                                                                              tttatttaTCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAAt                                                                                                         <  1:219177/141‑1 (MQ=255)       tatCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCatat                                                                                                   >  1:115542/1‑141 (MQ=255)                  aTGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACACAGAAATCCATATCATTAATGTAt                                                                                        >  2:92706/1‑141 (MQ=255)                    gagaCGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCa                                                                                      >  1:86250/1‑141 (MQ=255)                         ggAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGt                                                                                 <  1:41584/141‑1 (MQ=255)                         ggAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGt                                                                                 >  2:210179/1‑141 (MQ=255)                                 atatTGATATACATGCACCTAAAATGAATGATAATGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACAt                                                                         <  1:147699/141‑1 (MQ=255)                                  tatTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGTCAAAGAAATCCATATCATTAATGTATCAGATGTTATAACAtt                                                                        >  2:239280/1‑141 (MQ=255)                                        tataCATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGt                                                                  >  1:228355/1‑141 (MQ=255)                                                            atgaTAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAg                                              >  1:115743/1‑141 (MQ=255)                                                            atgaTAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAg                                              >  1:170758/1‑141 (MQ=255)                                                               aTAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCa                                           >  2:62368/1‑141 (MQ=255)                                                                                 ttaATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAAt                         >  1:28392/1‑141 (MQ=255)                                                                                                   tAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGAc       >  1:232725/1‑141 (MQ=255)                                                                                                      aCAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACttt    <  1:130531/141‑1 (MQ=255)                                                                                                        aaaTCACATACATTATTCGGATACATAGACAAAGAAATCTATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTTTAt  >  1:898/1‑141 (MQ=255)                                                                                                                       |                                                                                                                              TTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTTTAT  >  USA300TCH1516_ALE/2483257‑2483500

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑