Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,473	C→T	A67T (GCT→ACT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,473	0	C	T	100.0%	128.9 / NA	44	A67T (GCT→ACT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/25);  total (19/25)

CTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTG  >  USA300TCH1516_ALE/1744341‑1744598                                                                                                                                     |                                                                                                                              cTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTa                                                                                                                             >  2:57280/1‑135 (MQ=255)   ggTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAATGCCCATGCCCAGTGAATAAGTTACa                                                                                                                           >  2:138944/1‑135 (MQ=255)   ggTTTAATCGCATCTTTGTGCATCGTTAAACCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACAAGGTACTTTCCCTCCTATTCTAACAGCTGCAAAGCCAATCCCCATAGAATAGGTTACa                                                                                                                           >  2:228946/1‑135 (MQ=255)            gCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTATAGAACAGCCa                                                                                                                  >  1:328779/1‑135 (MQ=255)              aTCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAAt                                                                                                                >  1:534422/1‑135 (MQ=255)                      gCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTTTTTTACAAACTAACAGGTGCAAAGCCAATCCACATTGAATAAGTTACAGGAAAGCCAATGATAAAGc                                                                                                        >  1:454111/1‑135 (MQ=255)                        aTTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCa                                                                                                      <  1:527619/135‑1 (MQ=255)                        aTTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCa                                                                                                      <  1:298626/135‑1 (MQ=255)                           gTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATTCTCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCAcgc                                                                                                   <  1:619694/135‑1 (MQ=255)                                 aCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGTACAGCCAATGATAAAGCCACGCGCTTCa                                                                                             <  1:229652/135‑1 (MQ=255)                                 aCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCa                                                                                             <  1:411240/135‑1 (MQ=255)                                     ttGTACCATATTCTAGGTCATACTCATAACGAATAACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCAAATACCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTc                                                                                         >  1:590916/1‑135 (MQ=255)                                            atatTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAAc                                                                                  <  1:138944/135‑1 (MQ=255)                                               ttCTAGGTCATACTCATAACGAATGAATACACGAAAAAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAACCCACGCGCTTCAGGTCCTACAACgtt                                                                               >  1:13157/1‑133 (MQ=255)                                                 cTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGAGCCTATGGGCTTGCAACGatat                                                                             <  2:643246/135‑1 (MQ=255)                                                    ggTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACCGATGTCGTGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAATGTCACGCGTTTCAGGTCCTACAACGATATCaa                                                                          <  1:266442/135‑1 (MQ=255)                                                    ggTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCTTACAACGATATCaa                                                                          <  1:59109/135‑1 (MQ=255)                                                      tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGTTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTAAGGTACTAAAACAATATCAACa                                                                        >  2:101631/1‑135 (MQ=255)                                                      tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGGGCTTGAGGTCCTACAACGATATaaaaa                                                                        >  2:4651/1‑133 (MQ=255)                                                      tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGCTATCAAcc                                                                        >  2:556667/1‑134 (MQ=255)                                                       cATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACAt                                                                       <  2:119965/135‑1 (MQ=255)                                                         tACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACAtct                                                                     <  2:548472/135‑1 (MQ=255)                                                         tACTCATAACGAATGACTTCACGAGGTAATTGCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACAtct                                                                     <  2:319472/135‑1 (MQ=255)                                                            tCATACCGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                                  <  2:319032/135‑1 (MQ=255)                                                            tCAGAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                                  <  2:392600/135‑1 (MQ=255)                                                                    aaTGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGc                                                          >  2:384552/1‑135 (MQ=255)                                                                    aaTGACTTCACGAGGTAATTTCCCTTCTTTACTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTTCTTTGc                                                          >  1:499709/1‑135 (MQ=255)                                                                     aTGACTTCACGAGGTAATTTCCCTACTTTTCTAGCAGGTGCAACGCAAATACCCATATAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATAGCAACATCTCTGTCTTTTCCg                                                         >  2:177731/1‑135 (MQ=255)                                                                            cACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACTTCTCTGTCTTTTGCGTATTCTa                                                  <  1:570764/135‑1 (MQ=255)                                                                                                tttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAg                              <  1:599776/135‑1 (MQ=255)                                                                                                tttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGAACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCTTTTTTTACAGTTGTGTCTGTTGCAttg                              >  1:369239/1‑133 (MQ=255)                                                                                                       cAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAATGATATCAACATCTCTGTCTTTTGCGTATTCTTCATTTTTTTCTGTTGCATAGCCATATg                       <  1:57280/135‑1 (MQ=255)                                                                                                        atgTGCAAAACCAATCCTCATTGAATAAGTTCCATGACAGCCCATGCTAAAGCCACGCGCTTCAGGTCCTACAACTATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGc                      <  2:659101/133‑1 (MQ=255)                                                                                                        aGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGc                      <  2:87399/135‑1 (MQ=255)                                                                                                         ggTGCAAAGCCAATCCCACTGAAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCt                     >  2:434587/1‑135 (MQ=255)                                                                                                          gTGCAAAGCCAATCCCCATTGATTAAGTTACAGGACAGCCAATGATAACGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCtt                    <  2:250689/135‑1 (MQ=255)                                                                                                           tGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGTGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTc                   <  1:81440/135‑1 (MQ=255)                                                                                                             cAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACCATTTTATCTGTTTCATAGCCCTGTTCTTCAc                 >  2:415435/1‑135 (MQ=255)                                                                                                                 gCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCAtt             <  1:222461/135‑1 (MQ=255)                                                                                                                   cAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTAt           <  2:534422/135‑1 (MQ=255)                                                                                                                      tCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTTCAATTTTATCTGTTGCATAGCCATATGCTTAACCATTATcac        >  2:560691/1‑133 (MQ=255)                                                                                                                         ccATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATaa     <  1:583787/135‑1 (MQ=255)                                                                                                                           aTTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTTTTGCATAGTTATATGCTTCACCATTATCCATAAtt   <  1:487694/135‑1 (MQ=255)                                                                                                                            ttGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTg  >  2:457066/1‑135 (MQ=255)                                                                                                                                     |                                                                                                                              CTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTG  >  USA300TCH1516_ALE/1744341‑1744598

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑