Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,274,207	T→A	S204T (TCA→ACA)	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	1,274,207	0	T	A	100.0%	146.0 / NA	46	S204T (TCA→ACA)	codY	GTP‑sensing transcriptional pleiotropic repressor CodY
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (22/24);  total (22/24)

TGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAA  >  USA300TCH1516_ALE/1274077‑1274338                                                                                                                                   |                                                                                                                                    tGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACaaa                                                                                                                                 <  1:90390/135‑1 (MQ=255)     gaaGATAAAGAAGCGCGCGATAAAGCTGCTAGTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGtt                                                                                                                             >  2:331282/3‑135 (MQ=255)     gTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAAAAAAAGtt                                                                                                                             >  2:69866/1‑135 (MQ=255)             agcagCGCGCGATAAAGCTGCAATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATag                                                                                                                     >  1:189426/4‑135 (MQ=255)             agaagCGCGCGATAAAGCTGCTAATACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATag                                                                                                                     >  1:257589/1‑135 (MQ=255)              gaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATaga                                                                                                                    >  2:321283/1‑135 (MQ=255)                agtgcgcgATAAAGCCGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGt                                                                                                                  <  1:611833/132‑1 (MQ=255)                    cgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGTAACAAAAGTTGCAGATAGAGTTGGt                                                                                                              <  1:178427/135‑1 (MQ=255)                    cgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGt                                                                                                              >  1:32854/1‑135 (MQ=255)                     gcgATCAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTa                                                                                                             >  1:204422/1‑135 (MQ=255)                           aaGCTGCTATTACAATGGCAATTAATTCATTAACTAATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGGTAGAGTTGGTATTACTa                                                                                                       >  1:131076/1‑135 (MQ=255)                              ctgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAAGAAAAGTTGCAGATAGAGTTGGTATTACtggtt                                                                                                    >  2:533576/1‑131 (MQ=255)                               tgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGagc                                                                                                   <  1:18072/135‑3 (MQ=255)                                     tACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGATTTGGTATTACTAGATCTGTAAt                                                                                             <  1:616160/135‑1 (MQ=255)                                        aaTGGCAATTAATTCATTATCTTATGCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAtttt                                                                                          <  2:309781/135‑3 (MQ=255)                                         aTGGCAATTAATTCATTATCTTATTCTGAGAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTa                                                                                         <  2:365193/135‑1 (MQ=255)                                                  aattCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATATTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGAAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAAAGCACTa                                                                                >  1:88053/1‑135 (MQ=255)                                                    ttCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACtcaa                                                                              >  2:277786/1‑132 (MQ=255)                                                    ttCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGAACTACg                                                                              >  2:507590/1‑135 (MQ=255)                                                           tCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTa                                                                       >  2:559233/1‑135 (MQ=255)                                                            cTTAGTCGGAAAAAGAAGCGATTGAACATATCTGTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACGAGATCTGTAATTGTAAATGCACTACGTAAATTAg                                                                      <  2:32854/135‑1 (MQ=255)                                                             ttATTCTGAAAAAGAAGCGATTGAACCTATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGa                                                                     <  2:663773/135‑1 (MQ=255)                                                                 tCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCATTACGTAAATTAGAAAGt                                                                 <  1:336966/135‑1 (MQ=255)                                                                 tCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGt                                                                 >  2:199924/1‑135 (MQ=255)                                                                      aaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTTAATTAGAAAGTGCTgg                                                            <  1:492644/135‑1 (MQ=255)                                                                      aaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTgg                                                            <  2:547665/135‑1 (MQ=255)                                                                      aaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTgg                                                            <  1:134633/135‑1 (MQ=255)                                                                               gATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAACCGCAACAAAAGTTGCAGATAGAGTTCGTATTACTAGATCTTTAATTGTAAATGCACTACGTAAATTAGAAAGTCCTGGTGTAATTGa                                                   <  2:243167/135‑1 (MQ=255)                                                                                aTTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGaa                                                  >  2:404135/1‑135 (MQ=255)                                                                                aTTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGaa                                                  >  2:404084/1‑135 (MQ=255)                                                                                 ttGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAAt                                                 >  1:67063/1‑135 (MQ=255)                                                                                  tGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTCATTGAATc                                                >  2:53661/1‑135 (MQ=255)                                                                                   gAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCa                                               <  1:677108/135‑1 (MQ=255)                                                                                       attgcTTGGAACAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTTGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGtt                                           <  2:204422/131‑1 (MQ=255)                                                                                       atatCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGtt                                           <  2:177630/135‑1 (MQ=255)                                                                                        tatCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTc                                          >  1:389707/1‑135 (MQ=255)                                                                                                aagaaCTCGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGaa                                  <  2:559673/135‑1 (MQ=255)                                                                                                  gaaCTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTCAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATg                                >  2:161725/1‑135 (MQ=255)                                                                                                      ttGGCTGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAg                            <  1:652063/135‑1 (MQ=255)                                                                                                      ttGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAg                            <  1:112584/135‑1 (MQ=255)                                                                                                      ttGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTCCTTTAGGAATGAAAg                            <  1:346748/135‑1 (MQ=255)                                                                                                      ttGGCGGTACCGAAGTCATATTAATCGCAACCAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATTCACTAATTAAATTAGAAAGTGCTGGTGTTATTGAATCACGTTCTTTAGGAATGAAAg                            <  1:31712/135‑1 (MQ=255)                                                                                                                   aGGTCTATTAATCGCAACAAAAGTTGGAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTATAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaa               <  1:533576/135‑1 (MQ=255)                                                                                                                   aGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGTAATGAAAGGTACTTTCAATaa               <  1:314892/135‑1 (MQ=255)                                                                                                                          ttAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGACAGGTACTTTCATTAAAGTTaaa        >  2:566715/1‑135 (MQ=255)                                                                                                                                gCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaa  >  1:56497/1‑135 (MQ=255)                                                                                                                                   |                                                                                                                                    TGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAA  >  USA300TCH1516_ALE/1274077‑1274338

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑