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%	40.0 / NA	14	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (8/6);  total (8/6)

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCA  >  USA300TCH1516_ALE/1416326‑1416578                                                                                                                                     |                                                                                                                         aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                  >  2:139318/1‑141 (MQ=255) aCTCAATCATAGTAATCCCTCTTTAATTGTCTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTAAAATGATTAATATTACCTCGTTAAATGATTTAACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                  >  2:103364/1‑141 (MQ=255)                             gtgtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAATTTAt                                                                                      >  1:6882/1‑141 (MQ=255)                                         tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGAtaataa                                                                          <  1:162107/141‑1 (MQ=255)                                            ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaata                                                                       >  1:181446/1‑141 (MQ=255)                                            ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaata                                                                       <  1:55281/141‑1 (MQ=255)                                               gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                    <  2:138868/141‑1 (MQ=255)                                                                     atggtgaTACTTGAAAGGATTAATATTCCCTGGTTCAATGATTTGGCCTTCTTTTAAAACATAATTGTACTGACAATATTTTAATATATGACTTAAGTTATGTGGGATAATAAATAATGTTTGACCATGTTCTAATACAat                                              <  2:63193/135‑1 (MQ=255)                                                                     acgCTCATACGAGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAat                                              <  1:37144/139‑1 (MQ=255)                                                                       gCTCATACTTGAAATGATTAATATTACCTCGTTCAATAATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTAAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCCTGTTCTAATACAatat                                            >  1:55073/1‑141 (MQ=255)                                                                                 gAAATGATTAATATTACCTCGTTCACTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCACTACATGACTTACCTTATGTGTGATAATAAATCCTCTTTGACCATGTTCTAATACCATATGCtctcatca                                  >  2:238628/1‑134 (MQ=255)                                                                                             atTACCTCGTTCAATGATTTGACCGTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTCATACAATATGCCGTACTAAAACCATCGCtca                      >  2:58283/1‑139 (MQ=255)                                                                                                           tGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAg        >  2:83773/1‑141 (MQ=255)                                                                                                                 gACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCa  <  1:84465/141‑1 (MQ=255)                                                                                                                                     |                                                                                                                         ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCA  >  USA300TCH1516_ALE/1416326‑1416578

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: ‑