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%	51.3 / NA	22	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (14/8);  total (14/8)

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACT  >  USA300TCH1516_ALE/1416326‑1416589                                                                                                                                     |                                                                                                                                    aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTGGTTAGACAGACAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                             <  2:96498/141‑1 (MQ=255)   tCAATCATAGGAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                           <  2:30804/141‑1 (MQ=255)    cAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACATTCTTTTAAAACATAATTGTACTGACaa                                                                                                                          >  1:185435/1‑141 (MQ=255)                     ctTTAATTGTGTTCTATATTTTATTAGACGTTCAGTATACGGATGCAACTGCTCATACTTGAAATGATTAATATTACATCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTTACAATTTTTCAGTATATGatt                                                                                                         >  2:147318/1‑139 (MQ=255)                          aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                    >  2:117595/1‑141 (MQ=255)                               gtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATAACTTAAGTTAtgt                                                                                               >  2:106966/1‑141 (MQ=255)                               gtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTAACTAGTTCAATGATTTTACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATAAATTACGTTAtgt                                                                                               >  2:130235/1‑141 (MQ=255)                                                    tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATATATGACTTAAGTTATATGTGATAATAAATAATGtttaa                                                                          >  2:114911/1‑139 (MQ=255)                                                         ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTAGCTCGTGCAATGACTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                     >  2:135865/1‑141 (MQ=255)                                                         ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                     <  2:4717/141‑1 (MQ=255)                                                                tGCAAATGCTCATACTTGAAATGATTCATCATCTCCCGATCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAACATGTTCTAAt                                                              >  2:119342/1‑141 (MQ=255)                                                                tGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTAAAATTATGTGTGATAATAAATAATGTTTGACCATGTTATAAt                                                              >  2:155965/1‑141 (MQ=255)                                                                              cTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATACTTTATGATGGATCATGTTCTAATACAATATGCTGtaa                                                <  1:92860/141‑1 (MQ=255)                                                                                    aTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATc                                          >  1:26944/1‑141 (MQ=255)                                                                                       aTTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCAt                                       <  2:116302/141‑1 (MQ=255)                                                                                                aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCAATAACTTGAtt                              >  2:169569/1‑141 (MQ=255)                                                                                                     gTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGt                         <  2:108783/141‑1 (MQ=255)                                                                                                               ttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTAACTACCTGAGTTAATTTATGTGAGAGAATAAATAATGTTTGACCATGTTCTAATACAATATACTGTAATAAATCTATCACTTGATTACCGTTCAAAGCATc               >  2:153638/1‑141 (MQ=255)                                                                                                                  aCCTTCTTTTAAAACATAATTGGACGGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCaa            >  1:159621/1‑141 (MQ=255)                                                                                                                       cttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatgatg       >  2:106488/1‑141 (MQ=255)                                                                                                                        ttttAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGc      <  1:135865/141‑1 (MQ=255)                                                                                                                            aaaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACt  <  2:109152/141‑1 (MQ=255)                                                                                                                                     |                                                                                                                                    ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACT  >  USA300TCH1516_ALE/1416326‑1416589

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: ‑