Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	367,644	G→T	intergenic (‑96/‑62)	nanA ← / → bglK	N‑acetylneuraminate lyase/Beta‑glucoside kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	367,644	0	G	T	100.0%	109.1 / NA	32	intergenic (‑96/‑62)	nanA/bglK	N‑acetylneuraminate lyase/Beta‑glucoside kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (15/17);  total (15/17)

CAAAAGGAACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGTTT  >  USA300TCH1516_ALE/367500‑367780                                                                                                                                                 |                                                                                                                                         caAAAGGAACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCa                                                                                                                                       >  1:381172/1‑148 (MQ=255) caAAAGGAACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCa                                                                                                                                       >  2:187422/1‑148 (MQ=255)   aaaGGAACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCata                                                                                                                                     <  1:257581/148‑1 (MQ=255)        aaCGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATACCTTTTTGAAAATTGTATTCATATTTAt                                                                                                                                <  2:348298/148‑1 (MQ=255)                aCGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTAtaatt                                                                                                                        <  1:251628/148‑1 (MQ=255)                aCGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTAtaatt                                                                                                                        <  2:241266/148‑1 (MQ=255)                aCGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTAtaatt                                                                                                                        <  2:192578/148‑1 (MQ=255)                aCGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAATCCCTACAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTAtaatt                                                                                                                        <  2:63474/148‑1 (MQ=255)                           aaaCCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGt                                                                                                             >  1:215617/1‑148 (MQ=255)                           aaaCCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTAATGTATAATTAATGAAAATGt                                                                                                             >  2:297096/1‑148 (MQ=255)                               cTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGttttt                                                                                                         <  1:24754/148‑1 (MQ=255)                               cTTTTAAATATTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGttttt                                                                                                         <  2:259462/148‑1 (MQ=255)                                 tttAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTTATAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCa                                                                                                       >  2:123367/1‑148 (MQ=255)                                  ttAAATCTTTGTTCATGATGAAGTCCCTCCGAGAAACATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGGTTTTCaa                                                                                                      <  2:144938/148‑1 (MQ=255)                                       tCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAGCGCTATCATAAAATGTAATTGTATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCa                                                                                                 >  1:75577/1‑148 (MQ=255)                                                           ccTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAATCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAg                                                                             >  1:202716/1‑148 (MQ=255)                                                             tCCAGAAATCATTTGATAATATAGTTTACAGCTATAAGTGTAAGCGCTATCATAAAATGTAAGATTATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGgt                                                                           <  2:215920/148‑1 (MQ=255)                                                               cAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGgtgt                                                                         <  1:45003/148‑1 (MQ=255)                                                                  aaaTCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCGATCATAAAATGTAACAATATCTTTTTGAAAATTTTATTCATATTTATGTATAATTAATTAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTAtt                                                                      >  2:104681/1‑148 (MQ=255)                                                                          tGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCa                                                              <  1:5152/148‑1 (MQ=255)                                                                          tGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCa                                                              <  1:338502/148‑1 (MQ=255)                                                                           gATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTTTTTTTTTTTTTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCaa                                                             >  2:156594/1‑148 (MQ=255)                                                                           gATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCaa                                                             >  1:26807/1‑148 (MQ=255)                                                                                          aGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCa                                              >  2:313923/1‑148 (MQ=255)                                                                                                           cTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCa                             <  2:29357/148‑1 (MQ=255)                                                                                                                          aCAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCaa              <  1:217278/148‑1 (MQ=255)                                                                                                                          aCAATATCTTTTTGAAAATTCTATTAATAGGTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACAGCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCaa              <  1:82268/148‑1 (MQ=255)                                                                                                                              tatCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGa          >  2:81570/1‑148 (MQ=255)                                                                                                                                    ttttAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGt    >  2:194401/1‑148 (MQ=255)                                                                                                                                    tttGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGt    >  2:252922/1‑148 (MQ=255)                                                                                                                                     ttGAAAATTGTATTCATATTTATGTATACTTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTAGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGtt   >  1:144598/1‑148 (MQ=255)                                                                                                                                      tGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGttt  <  1:279190/148‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                         CAAAAGGAACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGTTT  >  USA300TCH1516_ALE/367500‑367780

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