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%	57.9 / NA	21	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (11/10);  total (11/10)

TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAAC  >  USA300TCH1516_ALE/1513795‑1514051                                                                                                                                        |                                                                                                                           tttatttGTATTTATAGATATATTAGTAACAAAAAAAATGAGGTTTGACTCGTGGAAAAAGAGTACAAAAAATACTGCAATAAAAGTACCACATAGGGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑t                                                                                                                      <  2:238940/141‑1 (MQ=255) tttatttGTATGTATCGCATTAATAATAGACATAAGAATAGGATTTGTATCTTAGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCATAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAttat                                                                                                                       <  2:119279/141‑3 (MQ=255) ttgagtggtatgtatCGGTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑t                                                                                                                      <  2:39008/134‑1 (MQ=255)                    ttattaGTAGCCATTGGAATGGGGTTTGTCTCGTAGATAAAGAGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCa                                                                                                   <  2:142088/141‑1 (MQ=255)                               cATTGGCATGGGGTTTGTCTCTTGGATAAAGAGTACAAAAAATACTGCAATAAAATTACCACATCACGTAAAAAAACCAACATCTATATAACTCATAATATGTTTTATTA‑TATTAGGATTATTAATGCCATTATTTCGAtt                                                                                        >  2:13427/1‑141 (MQ=255)                                 atGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                      <  2:101563/140‑1 (MQ=255)                                 atGGAATTGGGTTTGTCTCTTGTATAAAGCATACAAAAAATACTGCAATAAAAGTACCATATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                      <  2:183900/140‑1 (MQ=255)                                   ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATAGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTTTTTGCATTAtta                                                                                    >  1:220489/1‑139 (MQ=255)                                                  tctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCttcctttt                                                                     >  2:244615/1‑135 (MQ=255)                                                  tctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                     >  1:110851/1‑141 (MQ=255)                                                        aTAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTA‑TATTAGGATTATTAATGCCATTATTTTGATTATAACTTATCCTTGTATTTATAAtt                                                               >  2:172473/1‑141 (MQ=255)                                                             gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTCTAATTGAAtt                                                          >  2:223735/1‑141 (MQ=255)                                                                        aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatata                                               >  1:182932/1‑141 (MQ=255)                                                                                          cacaTCGCGTAAAAACCCCAGCATCTATATCACTCATAAGATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                             <  1:178930/141‑1 (MQ=255)                                                                                          cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                             <  1:17751/141‑1 (MQ=255)                                                                                              tCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATAACTTATCCTTTTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                         >  2:243143/1‑141 (MQ=255)                                                                                              tCGCGTAAAAAAACCAGCATCTATATAACTCAGAATATGTGTTATTA‑TATTAGGATTATTAATGCAATTATTTGGATTATCACTTATCCTTGTATTTATAATTCAATAATTATTATATATTAAACATCTTCATCATAAACa                         >  2:237824/1‑141 (MQ=255)                                                                                               gggtgaaaaaggCCAGCATCTATATCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTAGCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaa                        <  2:98234/136‑1 (MQ=255)                                                                                                           ccAGCATCTATATCACTCATAATATGTTTTCTTGATAGGAGG‑TGATTAATGCCATTATTTGGGTTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa            <  1:121590/141‑1 (MQ=255)                                                                                                                     tatCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAAc  >  2:194545/1‑141 (MQ=255)                                                                                                                     tatCACTCATAATATGTTTTATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTGATCTTTGTATTTATAATTGAATTAATATTATATATTAAAGATTGTCGTGCTAATTAATAATGTTATTAAATTTTTGaag  >  2:275407/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                           TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTG‑TATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAAC  >  USA300TCH1516_ALE/1513795‑1514051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑