Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,473	C→T	100%	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%	81.3 / NA	27	A67T (GCT→ACT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/15);  total (12/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAAT  >  USA300TCH1516_ALE/1744336‑1744596                                                                                                                                          |                                                                                                                            ttGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTAc                                                                                                                          <  1:198020/141‑1 (MQ=255)  tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACa                                                                                                                         <  2:138082/141‑1 (MQ=255)    aCCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATCCTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAgg                                                                                                                       <  1:205894/141‑1 (MQ=255)       tGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACa                                                                                                                    <  1:194218/141‑1 (MQ=255)        ggTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAg                                                                                                                   <  2:214120/141‑1 (MQ=255)                           gCATTGTTAACACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGACAggcg                                                                                                >  1:301767/1‑141 (MQ=255)                           gCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCAcgcg                                                                                                >  1:301761/1‑141 (MQ=255)                                   aaaaCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGt                                                                                        >  2:272431/1‑141 (MQ=255)                                     aaCATTGGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTcc                                                                                      <  1:238744/141‑1 (MQ=255)                                      aCATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCt                                                                                     >  1:91630/1‑141 (MQ=255)                                          ttGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACaa                                                                                 <  1:251709/141‑1 (MQ=255)                                            gTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGTTATTTTACCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTTAATAAGTTACAGGACAGCCAATGATAAAGCCACGCACTTCAGGTCCTACAACg                                                                               >  1:139280/1‑141 (MQ=255)                                            gTACCATATACTAGGTCATACTCATAACGAATGACTTCACGAGGTAACTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACg                                                                               >  2:230589/1‑141 (MQ=255)                                                    ttCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAAc                                                                       <  1:67634/141‑1 (MQ=255)                                                    ttCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAAc                                                                       <  1:110659/141‑1 (MQ=255)                                                    gtCTTGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAAc                                                                       <  2:357684/140‑1 (MQ=255)                                                           tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACATGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                                <  2:237615/141‑1 (MQ=255)                                                           tCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                                <  2:325534/141‑1 (MQ=255)                                                           tCATACTCAAAACTAAAGACTGCACGACGTAATTTCCCCTCTTTTCTAACAGCTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                                <  2:2630/141‑1 (MQ=255)                                                                           tGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTTCCATGCCATTCCCCATTGAATAATTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTCCAACGATATCAACATCTCTGTCTTTTGGGTATTCTa                                                >  1:134809/1‑141 (MQ=255)                                                                             aCTTCACGCGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCACCATTGAATAAGTTACAGGACAGCCAGTGATAAAGCCAAGCGCTTCAGGTCCTTCAACGATATCAACATCTCTGTCTTTTTCTTATGCAACa                                              >  2:36609/1‑141 (MQ=255)                                                                              cTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACaa                                             >  1:278712/1‑141 (MQ=255)                                                                                   cggggTAATTTCCCTTCTTTTCTAACAGGGTCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTa                                        <  2:193200/138‑1 (MQ=255)                                                                                     aGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATc                                      >  1:194740/1‑141 (MQ=255)                                                                                                               gTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCAt            <  1:326783/141‑1 (MQ=255)                                                                                                                   aaaGCCAATCCCCATTGAATAAGTTACAGGACAGCCACTGATAAAGCAACGCACATCAGGTCCTACAACGATATCAATATCTCTGTCTTTTGCGTATTCAACAATTTTCTCTGTTGCATAGCCATATGCTTCACCATTATc        >  2:140266/1‑141 (MQ=255)                                                                                                                         aaTCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAAt  >  1:140046/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                            TTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAAT  >  USA300TCH1516_ALE/1744336‑1744596

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: ‑