Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,191	C→A	A152S (GCA→TCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,191	0	C	A	100.0%	61.5 / NA	20	A152S (GCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (17/3);  total (17/3)

CACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATA  >  USA300TCH1516_ALE/2028069‑2028321                                                                                                                           |                                                                                                                                   caCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCaaa                                                                                                                  >  1:2586/1‑140 (MQ=255)                 tAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAAtt                                                                                                  >  1:135486/1‑141 (MQ=255)                 tAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCGGCACTTTACCTAAAATGTGTCTAACAACAATGGTATAATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATGTTTAGGCAGCGAAtt                                                                                                  >  2:176471/1‑141 (MQ=255)                   aaaaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAAGATGTAGGTCCCCAGTTct                                                                                                >  1:218847/1‑140 (MQ=255)                     aaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCACTATGTAGGTCGCCAATTCCAt                                                                                              >  1:133491/1‑141 (MQ=255)                                        aaTATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCAAATTCCATGTTGAATTTGTCCATATTc                                                                           >  1:148525/1‑141 (MQ=255)                                          tatTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTccc                                                                         >  1:105613/1‑141 (MQ=255)                                           atTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCa                                                                        >  2:236473/1‑141 (MQ=255)                                             tGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCACACt                                                                      >  2:206405/1‑141 (MQ=255)                                              gTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACtt                                                                     >  2:148585/1‑141 (MQ=255)                                               tAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTta                                                                    >  2:72238/1‑141 (MQ=255)                                                     aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACa                                                              >  1:44586/1‑141 (MQ=255)                                                      ccGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACaa                                                             >  2:258217/1‑140 (MQ=255)                                                                aaCCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGgtgt                                                   >  1:170160/1‑141 (MQ=255)                                                                                                    tgTATTATTTTACTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGa               <  1:73780/140‑1 (MQ=255)                                                                                                          attTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGa         <  2:210989/141‑1 (MQ=255)                                                                                                          attTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGAAAAATAAAGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGa         >  1:235289/1‑141 (MQ=255)                                                                                                              tCCTTACTATTTGAATCTTTTGTTAAGTCCCACTCTCTTTCGCTATTTCCATGTTCAATTTGTACATCTTCCCACTTATATACATAATCTCGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTc     <  2:148525/141‑1 (MQ=255)                                                                                                                 ttAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGCTGGTGAAGTCATa  >  2:225511/1‑141 (MQ=255)                                                                                                                 ttAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTCTTTAATAAAAGATGTTTAAGTCCTa  >  2:201308/1‑141 (MQ=255)                                                                                                                           |                                                                                                                                   CACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATA  >  USA300TCH1516_ALE/2028069‑2028321

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: ‑