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%	77.1 / NA	24	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (16/8);  total (16/8)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAAA  >  USA300TCH1516_ALE/1513807‑1514067                                                                                                                            |                                                                                                                                          tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACTGCAGTTAGAGAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                                          <  1:155803/141‑1 (MQ=255)         tattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACAAGCCTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                  >  2:97841/1‑141 (MQ=255)                       ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                    >  1:315849/1‑141 (MQ=255)                        gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATGCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCCTTATTTGGATTATCAc                                                                                                   >  1:157820/1‑141 (MQ=255)                        gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                                   >  1:74412/1‑141 (MQ=255)                          atggcatttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATAGCGTAAAAAAACCAGCATCTATATCACCCATAACATGTTTTATTGTATTAGCATTATTAAGGCCATTATTTGGATTATCACtt                                                                                                 <  2:108093/135‑1 (MQ=255)                                 ttGTCTCTTGGATAAAGCGTGCAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTGTATTGTATTAGGATTATTAATGCAATTATTTGGATTATCTCTTATCCTTg                                                                                          >  2:174971/1‑141 (MQ=255)                                   ctctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTAGATTATCACTTATCCTTGTa                                                                                        <  1:218600/140‑1 (MQ=255)                                             tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                        <  2:310674/131‑1 (MQ=255)                                             tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                        >  1:310674/1‑131 (MQ=255)                                               aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGat                                                                            >  1:171093/1‑140 (MQ=255)                                               aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                            >  1:336770/1‑141 (MQ=255)                                                aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                           >  1:261244/1‑141 (MQ=255)                                                   gTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTaa                                                                        >  2:348916/1‑141 (MQ=255)                                                        aacaaTACTCCAATAAAAGTACCACATCGCGTAAAATAACCATCATCTTTATCTCTTATAATTTGTTTTATTGTATTAGTATTATTAATGCCATTATTTTGATTATCTCTTATCCTTGTATTTATAATTGAATTAAtatta                                                                   <  2:171093/138‑1 (MQ=255)                                                        aaaaaTACTGCAATAAAAGTAACACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCCCGTAGTTATAATTGAATTAAtatta                                                                   >  2:161058/1‑141 (MQ=255)                                                                  cAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaaa                                                         >  1:331296/1‑140 (MQ=255)                                                                           tACCACCTCGCGTGAAAAAACCAGCATCTAGATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTg                                                <  2:319569/141‑1 (MQ=255)                                                                                            aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                               <  1:202490/141‑1 (MQ=255)                                                                                            aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGACATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                               <  1:28920/141‑1 (MQ=255)                                                                                               ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                            >  2:62407/1‑141 (MQ=255)                                                                                                cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                           >  2:162446/1‑141 (MQ=255)                                                                                                                    atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTATAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt       >  1:151908/1‑141 (MQ=255)                                                                                                                    atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt       >  1:234617/1‑141 (MQ=255)                                                                                                                         ttttATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACaaa  <  1:183300/141‑1 (MQ=255)                                                                                                                            |                                                                                                                                          TATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAAA  >  USA300TCH1516_ALE/1513807‑1514067

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: ‑