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%	59.8 / NA	23	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (16/7);  total (16/7)

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416326‑1416594                                                                                                                                     |                                                                                                                                         aCTCAATCATAATAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCCTTCAATGATTTGACCTTCTTTTAAAACATAATTTTACTg                                                                                                                                   >  2:77889/1‑140 (MQ=255)     aaTCATAGTAATCCATCTTTATGTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                               <  2:145744/140‑1 (MQ=255)              aaTCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAGATGCTCATACTTGCAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATAGTAATAACAATATTTCAAt                                                                                                                      >  1:113861/1‑140 (MQ=255)                                         tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataata                                                                                           >  2:114321/1‑140 (MQ=255)                                                aCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATCGTACTGACAATATTTCACTACCTGCCTTTAGGTATGGGTGATAATAAATAATg                                                                                    >  2:1384/1‑140 (MQ=255)                                                 cGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGt                                                                                   >  1:17207/1‑140 (MQ=255)                                                    tgaGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                                <  2:7182/138‑1 (MQ=255)                                                     cAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACTTTCTTTTAAAACATAATTGTAGTGACAATATTTCAATAGATGACTTAAGTTATGTGTGATAATAAATAATGTTTGa                                                                               >  2:2258/1‑140 (MQ=255)                                                                   aaaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATTTGTGATAATAAATAATTTTTTACCATGTTCtactac                                                                 >  1:111020/1‑140 (MQ=255)                                                                   aaaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAc                                                                 <  1:141169/140‑1 (MQ=255)                                                                          cATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGc                                                          >  2:186669/1‑140 (MQ=255)                                                                           aTACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCt                                                         <  1:246526/140‑1 (MQ=255)                                                                            tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATCATCTTTGACCATCTTCTAATCCAATATGCTg                                                        >  2:1223/1‑140 (MQ=255)                                                                                                     gTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAACATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAcca                               >  2:175863/1‑139 (MQ=255)                                                                                                       tCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGtt                             <  2:17207/140‑1 (MQ=255)                                                                                                        cAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGGCCATGTTCTAATACAATATGCTGTAATAATTCCATCACTTGATTACCGttg                            >  1:162798/1‑139 (MQ=255)                                                                                                        cAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCGGAAACAAATTCATCACTTAATTACCGTTc                            >  2:143742/1‑140 (MQ=255)                                                                                                          ctGATTTGCCCTTCATTTAAAAAATAATTGTACTGACAATATTTCAATCCATTACTTAAGTTATGTGAGATCATAAATAATATTTAACCATCTTCTCATACATTATGCTGTAAACAATACATCCCTTAATTACCttttca                          >  2:40598/2‑137 (MQ=255)                                                                                                                      tcttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatga              >  1:195287/1‑140 (MQ=255)                                                                                                                         tttAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGc           >  1:107179/1‑140 (MQ=255)                                                                                                                         tttAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTAATTACCCTTCAAACCATCCAATGACGc           >  2:51722/1‑140 (MQ=255)                                                                                                                           tAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCaa         <  1:186669/140‑1 (MQ=255)                                                                                                                                  tAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  <  1:90613/140‑1 (MQ=255)                                                                                                                                     |                                                                                                                                         ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416326‑1416594

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: ‑