Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	169,407	G→A	G82E (GGA→GAA)	repE →	Replication initiation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	169,407	0	G	A	100.0%	100.0 / NA	30	G82E (GGA→GAA)	repE	Replication initiation protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (15/15);  total (15/15)

CATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGT  >  USA300TCH1516_ALE/169280‑169540                                                                                                                                |                                                                                                                                      aaTTTATTAACGCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATATCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCaa                                                                                                                          <  1:30568/140‑1 (MQ=255)        taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  4:49732/1‑148 (MQ=255)        taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  4:149063/1‑148 (MQ=255)        taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  3:284589/1‑148 (MQ=255)           cTCACGAAGAAGGGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  4:353894/1‑148 (MQ=255)           cTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  4:347703/1‑148 (MQ=255)           cTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  4:269428/1‑148 (MQ=255)                 aagaagAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTg                                                                                                   <  3:16486/148‑1 (MQ=255)                 aagaagAGGAATGGGGAAATTTAGAAAGAAGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAAACAATTGAAAAAACAAATCGACTTTTg                                                                                                   <  4:15704/148‑1 (MQ=255)                         gAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                           <  4:313639/148‑1 (MQ=255)                         gAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                           <  4:186668/148‑1 (MQ=255)                                           aGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGa                                                                         <  3:228283/148‑1 (MQ=255)                                           aGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGa                                                                         <  3:401242/148‑1 (MQ=255)                                                      aaataaatATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCAc                                                              >  3:374490/1‑148 (MQ=255)                                                         taaataTATATATAAGTTGAAAAATATAGCTTCTATTGATTTGACAGATTTAAAAAAAATATCTTTAATAGAAAATGAAAAAAAAAAAAAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTa                                                           <  4:273444/148‑1 (MQ=255)                                                            atatAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGc                                                        >  4:29992/1‑148 (MQ=255)                                                              ataGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTc                                                      <  3:193226/148‑1 (MQ=255)                                                                agagATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCAt                                                    >  3:378276/1‑148 (MQ=255)                                                                      aaGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACtt                                              <  4:227705/148‑1 (MQ=255)                                                                         ttGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACAAAAGAACTATGTTCACTTATGCTCATCTACTTaaa                                           >  3:167143/1‑148 (MQ=255)                                                                         ttGAAAAATATAGCGTCTATTGATGTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTaaa                                           >  4:301220/1‑148 (MQ=255)                                                                            aaaaaTATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATa                                        >  4:261319/1‑148 (MQ=255)                                                                                   taGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATa                                        <  2:67295/141‑1 (MQ=255)                                                                                                tttGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGtttt                    >  3:254632/1‑148 (MQ=255)                                                                                                      aGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAag              <  3:25079/148‑1 (MQ=255)                                                                                                           tAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCCCTTATGTTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTaaa                >  1:29569/1‑141 (MQ=255)                                                                                                               gAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGaaa     <  3:203512/148‑1 (MQ=255)                                                                                                                aaaaTATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAACATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAAt    >  3:307348/1‑148 (MQ=255)                                                                                                                  aacatCTATAAGAGAAAAAGAAAACAAATAGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTAACTTATGATAATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGt  <  4:352056/145‑1 (MQ=255)                                                                                                                  aaTATCTTTAAAAGAAAATGAAATCCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGtt         <  2:53788/141‑1 (MQ=255)                                                                                                                                |                                                                                                                                      CATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGT  >  USA300TCH1516_ALE/169280‑169540

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: ‑