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Table 1 Codon sites with preference shifts detected with MutSelC60 and MutSelBC profiles, and sites identified in previous studies ([3] and [30])

From: Detecting amino acid preference shifts with codon-level mutation-selection mixture models

Site PIP (MutSelC60) PIP (MutSelBC) Finkelstein Tamuri Avian Human
44 0.0582 0.2155 0.966 YES A((S)) S((L))((A))
64 0.148 0.0170 0.954   M(I)((T)) T((M))((I))
76 0.00346 0    T((M))((K))((I))((A)) T
81 0.0165 0    T((I))((A)) M(V)((T))((I))
102 0.166 0.0000160    N((S))((K)) N
105 0.00535 0   YES T((A)) V(M)((T))((L))((I))
106 0.0184 1    T((A)) T(A)
107 0.0116 0.00637    S((N))((G)) S(N)
109 0.272 0.0005    V((I)) V(I)
122 0.0708 0.00608    V((M))((I))((A)) V((I))((F))
199 0.0278 1 0.997 YES A* S
249 0.445 0    E* E
271 0.0154 0.974 0.958   T((I))((A)) A((T))
292 0.0127 0.0265    I(V)((T))((M)) T((I))
338 0.0124 0    V((I))((A)) V(I)
377 0.00150 0.0655    A* A((V))((T))((E))
471 0.00383 0.0845    T((I))((A)) T((P))((I))((A))
475 0.69 1 0.994 YES L* M
493 0.00257 0.91   YES R* R((K))((G))
522 0.0516 0.008    Q* Q((H))
524 0.168 0.00547    T((M))((I)) T((I))
559 0.00799 0.26    T((M))((I))((A)) T(A)((S))((N))((I))
567 0.0852 0.216 0.977   D((N))((E)) N((D))
569 0.175 1   YES T* T(A)((S))
588 0.00283 0.00609 0.971   A((V))((T)) I((V))((A))
591 0.265 0.001    Q((L)) Q
613 0.0776 0.115   YES V((A)) T((V))((I))((A))
627 0.0111 0 0.977 YES E((K)) K((R))
661 0.00126 0.967   YES A((V))((T)) T((V))((A))
674 0.00644 0.0555 0.969   A((S)) T((P))((I))((A))
676 0.0165 0.242    T((I))((A)) I(T)
682 0.372 0   YES G* G(S)((N))
684 0.0596 0.999   YES A((T)) S(A)
702 0.552 1 0.955 YES K((R)) R((K))
711 0.17 0    N((S)) N
715 0.0916 0.00584    N((S)) N((T))
740 0.00239 0   YES D* D((N))
754 0.0125 0.0335    I* I((S))((F))
  1. Sites with a preference shift, defined as a PIP below the detection threshold of 0.05, are in bold. Amino acids have no parentheses if their frequencies are greater than 0.5, one set of parentheses if between 0.1 and 0.5, and two sets if between 0.01 and 0.1. An asterisk on a single amino acid indicates that other amino acids are present at a frequency of less than 0.01