Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	790,778	G→A	100%	intergenic (+277/‑197)	USA300HOU_0741 → / → USA300HOU_0742	possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	790,778	0	G	A	100.0%	35.9 / NA	13	intergenic (+277/‑197)	USA300HOU_0741/USA300HOU_0742	possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (9/4);  total (9/4)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTAA  >  CP000730/790647‑790914                                                                                                                                    |                                                                                                                                         gAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCaaa                                                                                                                                 >  1:269972/1‑141 (MQ=255)               aTTACTCTATATTTATTAATTGAGCTATGCTTGTTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTCAAta                                                                                                                   >  2:118676/1‑140 (MQ=255)                      tataTTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAACTAAAGAAACTGACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTg                                                                                                            >  1:255808/1‑141 (MQ=255)                             attaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATAAAAGTTGAAAGCTa                                                                                                     >  2:57610/1‑141 (MQ=255)                                                                       ttAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACt                                                           <  2:68278/141‑1 (MQ=255)                                                                        tAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACta                                                          <  1:46338/141‑1 (MQ=255)                                                                         aaaTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACtat                                                         >  1:185441/1‑141 (MQ=255)                                                                           aTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATaa                                                       >  2:99923/1‑141 (MQ=255)                                                                                       aaTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGt                                           >  1:35267/1‑141 (MQ=255)                                                                                                      taaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGcc                            >  2:139402/1‑140 (MQ=255)                                                                                                                      aGCAAATATGAGTTATAGCCCAAAATACTTGGTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTAc            <  1:99923/141‑1 (MQ=255)                                                                                                                               gAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTa   <  1:7618/141‑1 (MQ=255)                                                                                                                                aGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTaa  >  1:268871/1‑141 (MQ=255)                                                                                                                                    |                                                                                                                                         GAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTAA  >  CP000730/790647‑790914

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑