Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,274,220	A→G	D208G (GAT→GGT)	codY →	GTP‑sensing transcriptional pleiotropic repressor CodY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,274,220	0	A	G	100.0%	54.3 / NA	15	D208G (GAT→GGT)	codY	GTP‑sensing transcriptional pleiotropic repressor CodY
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (8/7);  total (8/7)

AAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAGATGAATTAGAAA  >  USA300TCH1516_ALE/1274087‑1274360                                                                                                                                      |                                                                                                                                             aaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTa                                                                                                                                >  1:96046/1‑148 (MQ=255) aaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGGATTa                                                                                                                                >  1:202607/1‑148 (MQ=255)       gcgcgcGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGAt                                                                                                                          <  1:105690/148‑1 (MQ=255)       gcgcgcGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGAt                                                                                                                          >  1:109908/1‑148 (MQ=255)                                               tATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTgg                                                                                  <  1:188796/148‑1 (MQ=255)                                               tATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTgg                                                                                  <  1:24845/148‑1 (MQ=255)                                                             aaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCAc                                                                    >  1:196375/1‑148 (MQ=255)                                                             aaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTAAGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCAc                                                                    >  1:239716/1‑148 (MQ=255)                                                                     gATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTa                                                            <  1:84936/148‑1 (MQ=255)                                                                              tatCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGaaa                                                   <  1:254639/148‑1 (MQ=255)                                                                                              ggCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAg                                   <  1:122431/148‑1 (MQ=255)                                                                                                                     cGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAGAt            >  1:196544/1‑148 (MQ=255)                                                                                                                     cGCATCAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATAACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTATTAGAt            >  1:229904/1‑148 (MQ=255)                                                                                                                           aaaaGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAGATGAATTa      <  1:88032/148‑1 (MQ=255)                                                                                                                               gTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAGATGAATTAGaaa  >  1:61643/1‑148 (MQ=255)                                                                                                                                      |                                                                                                                                             AAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAGATGAATTAGAAA  >  USA300TCH1516_ALE/1274087‑1274360

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: ‑