Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	677,191	C→T	P23L (CCG→CTG)	USA300HOU_RS03265 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	677,191	0	C	T	100.0%	63.4 / NA	18	P23L (CCG→CTG)	USA300HOU_RS03265	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (10/8);  total (10/8)

TTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGATTCAAAGGAATTTGTTTGCTTT  >  USA300TCH1516_ALE/677046‑677329                                                                                                                                                  |                                                                                                                                           ttAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGc                                                                                                                                          <  1:3752/148‑1 (MQ=255) ttAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATATTTAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGc                                                                                                                                          <  1:146904/148‑1 (MQ=255)                tGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGata                                                                                                                           <  1:65967/148‑1 (MQ=255)                             ttAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGt                                                                                                              <  1:109729/148‑1 (MQ=255)                              tAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTa                                                                                                             <  1:4955/148‑1 (MQ=255)                                                   gATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCt                                                                                        >  1:98453/1‑148 (MQ=255)                                                   gATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCt                                                                                        >  1:261970/1‑148 (MQ=255)                                                          cATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAaaaga                                                                                 <  1:209970/148‑1 (MQ=255)                                                          cATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAaaaga                                                                                 >  1:7993/1‑148 (MQ=255)                                                                  aGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCaa                                                                         >  1:266956/1‑148 (MQ=255)                                                                                                    ttACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGcac                                       >  1:248536/1‑148 (MQ=255)                                                                                                                   gaagaTTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGa                        <  1:126939/148‑1 (MQ=255)                                                                                                                    aagaTTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGAt                       >  1:246524/1‑148 (MQ=255)                                                                                                                    aagaTTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGAt                       >  1:240605/1‑148 (MQ=255)                                                                                                                     agaTTACTTTAATCATAAAGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGAtt                      >  1:287906/1‑148 (MQ=255)                                                                                                                                     aaaGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGATTCAAAGGAAtttgtttg      >  1:57868/1‑148 (MQ=255)                                                                                                                                     aaaGGTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGATTCAAAGGAAtttgtttg      >  1:78002/1‑148 (MQ=255)                                                                                                                                         gTTTATCACTGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGATTCAAAGGAATTTGTTTGCttt  <  1:108022/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                           TTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCATATTAATGATTCAAAGGAATTTGTTTGCTTT  >  USA300TCH1516_ALE/677046‑677329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑