Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,513,930	A→T	100%	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%	130.4 / NA	39	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (21/18);  total (21/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTA  >  USA300TCH1516_ALE/1513800‑1514063                                                                                                                                   |                                                                                                                                      ttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTa                                                                                                                              >  2:148784/1‑140 (MQ=255)    tatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGa                                                                                                                           <  1:446436/140‑1 (MQ=255)    tatcgatCGCTTTAGTAGTAGCCATTGGCATGGGGTTTGTCGCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACTACATCGCGTAAAAAAACCAGCATCTACATCACTCCTAATATGTTTTATTGTATTAGGa                                                                                                                           <  1:230597/135‑1 (MQ=255)           cgatttATAAGTAGCCATTGGCATGAGGTTTGTCACTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTaa                                                                                                                    <  2:162818/137‑1 (MQ=255)            gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCCTAATATGTTTTTTTGTATTAGGATTATTAAt                                                                                                                   >  1:481398/1‑140 (MQ=255)                tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                               >  2:12242/1‑140 (MQ=255)                tattaGTAGCCATGGGAATGGGGTTTGTATCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                               <  2:522632/140‑1 (MQ=255)                    agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                           >  1:232897/1‑140 (MQ=255)                       agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTCTATTGTATTAGGCTTCTTATTGACATTATTTg                                                                                                        >  2:57533/1‑140 (MQ=255)                        gCCATTGTGATTGGGTTTGTCTCTTGGACAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                       <  2:344801/140‑1 (MQ=255)                        gCCAGTGGCATGGCGTATGTATCTTAGATAAAGAGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                       <  2:99219/140‑1 (MQ=255)                           aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGAtt                                                                                                    <  1:34056/140‑1 (MQ=255)                             tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTAACACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                  >  1:202870/1‑140 (MQ=255)                                      gTTTGTCTCTTGAATAAATCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATcc                                                                                         <  2:313595/140‑1 (MQ=255)                                       tttGTCTCTTGTATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCt                                                                                        <  1:30322/140‑1 (MQ=255)                                       tttGTCTCTTGGAGAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCt                                                                                        <  1:362093/140‑1 (MQ=255)                                              ctTAGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACAACACGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                 <  2:321326/140‑1 (MQ=255)                                                      aaGCGTACAAAAAATACTGCAATAAAGGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                         >  2:218266/1‑140 (MQ=255)                                                        gCGTACAAAAAATACTGCAATAAAAGTACAACATCGCGT‑AAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                      <  1:362796/140‑1 (MQ=255)                                                            aCAAAAAATAGTGCAATAAAACTACCACATTGCGTAAAAAAACCAGTATCTATATCACGCATAATATGTTTTATTGTATTAGGATTATTAATGCCATGATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAat                                                                   <  2:122870/140‑1 (MQ=255)                                                             cAAAAAATACTGCAATAAGAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAata                                                                  <  1:98111/140‑1 (MQ=255)                                                             cAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAata                                                                  >  2:444175/1‑140 (MQ=255)                                                                  aaTACTGCAATAAAAGTACCACATACCGTAAAATAACCAGTAAACCAGGCACTCGTTATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                                             <  1:527956/140‑1 (MQ=255)                                                                      cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATAtt                                                         >  1:107137/1‑140 (MQ=255)                                                                      cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATAtt                                                         >  1:241856/1‑140 (MQ=255)                                                                         cAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaa                                                      >  2:198657/1‑140 (MQ=255)                                                                                    ccACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                           >  2:524586/1‑140 (MQ=255)                                                                                     cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCt                                          >  1:46388/1‑140 (MQ=255)                                                                                         tCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                                      >  1:477317/1‑140 (MQ=255)                                                                                            cgTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCCCTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTCCTACACaat                                   >  2:77881/1‑140 (MQ=255)                                                                                                     aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                          <  2:285132/140‑1 (MQ=255)                                                                                                     aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                          <  1:260842/140‑1 (MQ=255)                                                                                                      ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTTTTTGGAAACCAACTACTATTCTATATTTAAGATCGTCGTGCTAAACAAAAATGCACtaa                         >  1:227490/1‑138 (MQ=255)                                                                                                         gCATCTATATCACTCATAATATGTTTTATTGTCTTAGGATTATTACTGCCATTATTTGGCTTCTCACTTATCCTTGTATTTATACTTGACTTCATATTATATATTAAAGCTCTTCGTGCTAAACAATAATCCACTTACAg                      >  1:130176/1‑140 (MQ=255)                                                                                                         gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAg                      >  1:304186/1‑140 (MQ=255)                                                                                                                tatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCTTGCTAAACAATAATGCACTTAAATttttaca               >  2:394748/1‑137 (MQ=255)                                                                                                                  tCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACt             <  1:191275/140‑1 (MQ=255)                                                                                                                        ataataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaa       >  1:445914/1‑140 (MQ=255)                                                                                                                             atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATATTGCACTTAAAGTTTTGAACTGACGAAATTTa  >  2:340069/1‑140 (MQ=255)                                                                                                                                   |                                                                                                                                      TTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTA  >  USA300TCH1516_ALE/1513800‑1514063

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: ‑