Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,416,458	A→T	I216N (ATT→AAT)	oppD_4 ←	Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,416,458	0	A	T	100.0%	47.1 / NA	17	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (6/11);  total (6/11)

TAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416324‑1416590                                                                                                                                        |                                                                                                                                     tAACTCAATCATAGTAATCCCACTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACt                                                                                                                                <  2:33712/141‑1 (MQ=255)   aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                              >  1:45682/1‑141 (MQ=255)      cAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                           <  1:150357/141‑1 (MQ=255)            tattAATCCCGCTTTAATGGTGTTCTGTATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAGACATAATTGTACTGACAATATTTc                                                                                                                     <  2:173694/138‑1 (MQ=255)                       ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACt                                                                                                          >  1:85404/1‑141 (MQ=255)                         ttAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTa                                                                                                        <  1:153246/141‑1 (MQ=255)                            aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCTACACTT‑AAATTATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                     <  1:162049/141‑1 (MQ=255)                                           tAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGAtaataa                                                                                      <  1:159519/141‑1 (MQ=255)                                             aTTAGACGTTCAGTCTACGGATTCAAATGCTC‑ATACTTGAAATGATTAATAGTACCTCGTTCAATGATTTGACCTTCTTTTAACACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                    <  2:149924/141‑1 (MQ=255)                                                                                     aaaTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATaaa                                             >  1:224191/1‑141 (MQ=255)                                                                                          aTTAATATTACCTCGTTCAATGATTAGACCTTCTTTTAAAACATAATTGTAATGACAATATTTCAATACATTACTTACCTTATGTGTAATAATAAATAATGTTTTACACTATTCTATTACAATATGCGTTAACAAATCAAt                                        >  2:162844/1‑141 (MQ=255)                                                                                                 ttACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGa                                 <  2:45682/141‑1 (MQ=255)                                                                                                         taaaaTGATTTGATCTTCTTTTAAAACATAATTGTACTGACAATATTTCATTACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGtt                         <  2:223113/138‑1 (MQ=255)                                                                                                            aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCGATCACTTGATTACCGTTCaa                      >  2:178192/1‑141 (MQ=255)                                                                                                                        ttcttTTAAAATATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatga          <  2:142547/141‑1 (MQ=255)                                                                                                                           ttttAAAACATAATTATAATGACAATTGTACAATAGATGACGTAAGTTATGTGTGATAATAATTAATGTTTGACCATGTTCTAATACAATATGCTGTAATAACTCCATTACTTGTTTACGATTCATCGCATCTAATGATGc       <  2:131948/141‑1 (MQ=255)                                                                                                                                aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATCCAACTg  >  2:90106/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                                     TAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTC‑ATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416324‑1416590

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: ‑