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%	40.0 / NA	14	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 (5/9);  total (5/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATG  >  CP000730/790666‑790910                                                                                                                 |                                                                                                                                     tctATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGt                                                                                                          <  1:233322/141‑1 (MQ=255) tctATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGt                                                                                                          <  1:160667/141‑1 (MQ=255)              aTTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGCTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACaaa                                                                                             >  2:183587/1‑141 (MQ=255)                 gAGCTATGCTTATGATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATaa                                                                                          <  2:115225/141‑1 (MQ=255)                             ttattaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATaa                                                                              >  1:11178/1‑141 (MQ=255)                                ttaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACt                                                                           <  1:114501/141‑1 (MQ=255)                                  aCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTg                                                                         <  2:112459/141‑1 (MQ=255)                                        tGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTg                                                                   <  1:15732/141‑1 (MQ=255)                                                        aTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATaa                                                   >  2:46098/1‑141 (MQ=255)                                                               aaTTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGAc                                            <  1:206097/141‑1 (MQ=255)                                                                   gAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGATTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATg                                        <  2:22671/141‑1 (MQ=255)                                                                             atTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTa                              <  1:113845/141‑1 (MQ=255)                                                                                                         tatGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGACAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATg  >  1:191515/1‑141 (MQ=255)                                                                                                         gatGAGATATAGCCCAAAAGACTTGTTAAATCAAATTTGAAAGCGACAAGTAACGAAAATTAGAAACATGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTAAAACGCACTTATTAATTAACTACATAATg  >  2:250312/2‑141 (MQ=255)                                                                                                                 |                                                                                                                                     TCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATG  >  CP000730/790666‑790910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑