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	95.8%	70.7 / NA	24	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (10/13);  total (11/13)
Fisher's exact test for biased strand distribution p-value = 4.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGA  >  USA300TCH1516_ALE/1513806‑1514057                                                                                                                             |                                                                                                                                gtatAGCTTAATTAGTAGCAGGTGGAATGGGGGATGTATTGTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattat                                                                                                                 <  2:230992/141‑1 (MQ=255)       cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAttc                                                                                                           >  2:53194/1‑139 (MQ=255)         ttataaGTAGCCAATGGCATGGGGTTTGTCTCTTGAATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                         <  2:277339/141‑1 (MQ=255)             tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                     <  1:106280/141‑1 (MQ=255)             tagtagCCATTGGAATGGGGTTGGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                     <  1:176179/141‑1 (MQ=255)                       tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                           <  1:325150/141‑1 (MQ=255)                        gagaTGGAGTTTGTCTATTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                          <  2:331806/138‑1 (MQ=255)                                      atattGGAAAAAGAGTAAAAAAAAGAATGCAATAAAAGTACCAAATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                            <  2:277991/138‑1 (MQ=255)                                                aaGCGTACAAAAAATACTTCAATAAAAGTACCACATCGCGTAAAATAATCTGTTTCTTGTTCAATCCTTCTTTGTGTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                  <  2:174055/141‑1 (MQ=255)                                                aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                  <  2:160347/141‑1 (MQ=255)                                                     tACAAAAAATACGGCAATAAAAGTGACACATTGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGTCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAat                                                             <  2:221393/141‑1 (MQ=255)                                                     aaaaaaaaaTACTGCAATAAAAGTACCACATCTCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAat                                                             <  2:120074/138‑1 (MQ=255)                                                         aaaaaTACTGTAATAAAAGTAACACATGGCGTAAAAAAAACAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                         <  2:183108/141‑1 (MQ=255)                                                          aaaaTACTGCAATAACAGTTCCTCAGCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                        >  2:129529/1‑141 (MQ=255)                                                           aaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                                       >  1:291313/1‑141 (MQ=255)                                                                            tACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTg                                      >  2:72293/1‑141 (MQ=255)                                                                             aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTCGGATTCTTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                     >  1:3477/1‑141 (MQ=255)                                                                             aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                     >  1:351961/1‑141 (MQ=255)                                                                                    cgcgTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTAGGAATATCATTATTCATAATATTTATAATTGAATTAATATTATATATTAAAGAACGTCGTGCTAAACaa                              >  1:223471/1‑141 (MQ=255)                                                                                             aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAATATCGTCGTGCTAAACAATAATGCACt                     <  2:254009/141‑1 (MQ=255)                                                                                              aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAACACAATATAGTAAAGATCGTCGTGCTAAACAATAATGCACtt                    >  1:65673/1‑141 (MQ=255)                                                                                                 cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                 >  2:293899/1‑141 (MQ=255)                                                                                                   gCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGTTAAACAATAATGCACTTAAAGt               >  1:68492/1‑141 (MQ=255)                                                                                                                tCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGa  >  1:270146/1‑141 (MQ=255)                                                                                                                             |                                                                                                                                GTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGA  >  USA300TCH1516_ALE/1513806‑1514057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑