Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,269	G→C	P126A (CCA→GCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,269	0	G	C	100.0%	71.0 / NA	19	P126A (CCA→GCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (10/9);  total (10/9)

ACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACG  >  USA300TCH1516_ALE/2028144‑2028399                                                                                                                              |                                                                                                                                   aCCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCAcc                                                                                                                     <  1:163893/141‑1 (MQ=255)             tCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTg                                                                                                         >  1:257461/1‑141 (MQ=255)              cTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGt                                                                                                        <  1:110559/141‑1 (MQ=255)                  caacaaTGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTtaa                                                                                                    <  1:156719/141‑1 (MQ=255)                        tGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAg                                                                                              >  1:154449/1‑141 (MQ=255)                         ggTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGa                                                                                             >  1:233614/1‑141 (MQ=255)                              tattTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTg                                                                                        <  1:36327/141‑1 (MQ=255)                                      ttAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATa                                                                                >  1:251452/1‑141 (MQ=255)                                               gCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTCCGTTGCTAACAAACACGCTATGCCATTGTAAAAGATTTTGAAGTCATAACCTCAGcc                                                                       >  1:76207/1‑141 (MQ=255)                                               gCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATcc                                                                       >  1:377653/1‑141 (MQ=255)                                                        gTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAact                                                              >  1:173513/1‑141 (MQ=255)                                                         ttAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAacta                                                             >  1:271063/1‑141 (MQ=255)                                                               cAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACttttt                                                       >  1:327393/1‑141 (MQ=255)                                                                             ccAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTtg                                         >  1:19230/1‑141 (MQ=255)                                                                                 ttCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTa                                     <  1:57103/141‑1 (MQ=255)                                                                                    cATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTa                                  <  1:47711/141‑1 (MQ=255)                                                                                    cATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTa                                  <  1:47819/141‑1 (MQ=255)                                                                                               tGTACATCTTCCCACTTATATACATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGcaca                       <  1:220325/141‑1 (MQ=255)                                                                                                                    aCATAAACTGCTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACg  <  1:361492/141‑1 (MQ=255)                                                                                                                              |                                                                                                                                   ACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACG  >  USA300TCH1516_ALE/2028144‑2028399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑