Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,513,930	A→T	L413F (TTA→TTT)	USA300HOU_RS07375 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,513,930	0	A	T	100.0%	68.5 / NA	23	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (13/10);  total (13/10)

ATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATT  >  USA300TCH1516_ALE/1513808‑1514061                                                                                                                           |                                                                                                                                    atCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAATAAACCAGCATCTATATCACTCTTAATATGTTTTATTGTATTAGGa                                                                                                                         <  1:511797/135‑1 (MQ=255)         attaATAACCATGGGCATGGGGCTTGCCCCCTAGATAAAGCGTACAAAAAATACCGCAATAAAAGTACCACATCGAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                 <  2:348581/135‑1 (MQ=255)            agcagCCAGTGGCATGGGTCTTGTCTCTTGGACAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCTTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                              <  1:135116/132‑1 (MQ=255)             gtagCCATTGCCATCGGGATTGTCTCTTGGATAAAGCATACAAGAAATACTGCAATCAACGTGCCACATAGCGTAAAACAACCAGTATCTATATCACTCATAATATGTTTTATTGTATTAGGATTCTTAATGCCa                                                                                                             >  1:472982/1‑135 (MQ=255)              tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                            >  1:476801/1‑135 (MQ=255)              tagCCATTGGCATGGGGATTGTCTCTTGGATAAAGCGTACAAAAAATAATGCAATAAAAGTACAACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                            >  1:616328/1‑135 (MQ=255)                          tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACCTTGCTTTAAAAAACCAGCATCTTTATCACTTTTAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                <  1:266970/135‑1 (MQ=255)                          tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                <  2:325732/135‑1 (MQ=255)                            gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                              >  1:576437/1‑135 (MQ=255)                             ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACAGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                             >  1:60991/1‑135 (MQ=255)                                 tGTCTCTTGGATAAAGCGTACAAAAAATACTACAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                         >  1:474085/1‑135 (MQ=255)                                      ctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTTTTTGTATTATCACTTATCCTTg                                                                                    <  1:477441/135‑1 (MQ=255)                                             aaaGTGCACAAAAAATACTGGAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtat                                                                             <  2:273867/135‑1 (MQ=255)                                             aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAAACAGTTATTCTATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTTTTTGGATTATCACTTATCCTTGTATTtat                                                                             <  1:659590/135‑1 (MQ=255)                                               aGCGTACAAAAAACACTGCAATAAAAGTACCACATCGCGTAAAAAATCCGGCTTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                           <  1:615201/135‑1 (MQ=255)                                                                                       aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:501575/1‑135 (MQ=255)                                                                                       aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:60269/1‑135 (MQ=255)                                                                                       aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:316295/1‑135 (MQ=255)                                                                                       aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:268818/1‑135 (MQ=255)                                                                                               cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATCTTAAAGATCGTCGTGTTAAACAATAATGCa                           >  2:608464/1‑135 (MQ=255)                                                                                               cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTACTGCTAAACAATAATGCa                           >  2:617365/1‑135 (MQ=255)                                                                                                     cTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                     >  1:593346/1‑135 (MQ=255)                                                                                                           cACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTACAGTTTTg               <  2:60991/135‑1 (MQ=255)                                                                                                                        ttttATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt  >  1:47642/1‑135 (MQ=255)                                                                                                                        ttttATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt  >  2:89725/1‑135 (MQ=255)                                                                                                                           |                                                                                                                                    ATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATT  >  USA300TCH1516_ALE/1513808‑1514061

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: ‑