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	96.7%	97.2 / NA	30	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (15/14);  minor base C (0/1);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACATGTTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTCGTCTG  >  USA300TCH1516_ALE/1416316‑1416599                                                                                                                                               |                                                                                                                                               caatattttAACTCAATCCTAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACt                                                                                                                                         <  1:254161/144‑1 (MQ=255)          aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATAtt                                                                                                                                >  1:555475/1‑149 (MQ=255)          aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGCTCCGAGCTCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATAtt                                                                                                                                <  1:589678/149‑1 (MQ=255)                  cATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTAACAATATTTCAATACa                                                                                                                        <  1:427482/149‑1 (MQ=255)                    tAGTAATCCCTCTTTCATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATg                                                                                                                      <  1:374515/149‑1 (MQ=255)                    aaGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGACTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATg                                                                                                                      <  1:272381/148‑1 (MQ=255)                          tCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGCTGCACATGATCATACTTGAAATGATTAATATTACATCGTTCAATGATTTGACCTCCTTTTAAAACAGAATTA‑TACTGACAATATTTCAATACATGACTTaa                                                                                                                >  2:593073/1‑149 (MQ=255)                              tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTa                                                                                                            >  1:83585/1‑149 (MQ=255)                               ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                           >  1:184663/1‑149 (MQ=255)                               ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                           <  2:387699/149‑1 (MQ=255)                                  ttatttggtTCTATATTTAATTAGACGTTCATTATATGTATGCATAGTGTGATACTTGAAAGGATTAATATTCCCACGGTCCATGTTTTGATCTTCCTATAAATC‑TCACTGTTACTGTCAATCTTTCTATACATGGCGTAAGTTAtatg                                                                                                        <  2:112586/142‑1 (MQ=255)                                                    aaTTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGttt                                                                                      >  1:221395/1‑149 (MQ=255)                                                         gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                                 >  2:46188/1‑149 (MQ=255)                                                             ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                             <  1:377960/149‑1 (MQ=255)                                                              tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTc                                                                            <  1:272947/149‑1 (MQ=255)                                                                  tataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAAt                                                                        <  2:601263/149‑1 (MQ=255)                                                                     aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                                     <  2:470442/149‑1 (MQ=255)                                                                      cGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACaa                                                                    >  1:262960/1‑149 (MQ=255)                                                                             aactGCTCATAGTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTg                                                             <  1:80331/146‑1 (MQ=255)                                                                             aaaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACAGGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATCAAatatcatg                                                             >  2:231570/1‑145 (MQ=255)                                                                               aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAGTACATTACTTAAGTTGCGTCAGTAAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGta                                                           <  1:593073/149‑1 (MQ=255)                                                                                  cTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaata                                                        >  1:108943/1‑149 (MQ=255)                                                                                        cTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCa                                                  >  2:308748/1‑149 (MQ=255)                                                                                         ttGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCAt                                                 >  2:254585/1‑149 (MQ=255)                                                                                                    aaTATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAc                                      >  2:436580/1‑149 (MQ=255)                                                                                                          aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                                <  2:130705/149‑1 (MQ=255)                                                                                                             tCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGGTTACCGTTCAAAg                             >  1:475076/1‑149 (MQ=255)                                                                                                                 tCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATc                         >  1:503866/1‑149 (MQ=255)                                                                                                                    aTGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCaa                      >  1:64444/1‑149 (MQ=255)                                                                                                                                        aaCATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTTATTACCGTTCAAAGCATCCAATGATGCAACTGGTGCGTCTg  <  2:184663/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                               ACATGTTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTCGTCTG  >  USA300TCH1516_ALE/1416316‑1416599

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑