diff --git a/R/Gene_Centric_Coding_Info.R b/R/Gene_Centric_Coding_Info.R
index 71c265b..febdb32 100644
--- a/R/Gene_Centric_Coding_Info.R
+++ b/R/Gene_Centric_Coding_Info.R
@@ -87,14 +87,14 @@ Gene_Centric_Coding_Info <- function(category=c("plof","plof_ds","missense","dis
 	
 	if(category=="ptv")
 	{
-		results <- info_synonymous(chr=chr,genofile=genofile,obj_nullmodel=obj_nullmodel,gene_name=gene_name,known_loci=known_loci,rare_maf_cutoff=rare_maf_cutoff,
+		results <- info_ptv(chr=chr,genofile=genofile,obj_nullmodel=obj_nullmodel,gene_name=gene_name,known_loci=known_loci,rare_maf_cutoff=rare_maf_cutoff,
 		                           method_cond=method_cond,QC_label=QC_label,variant_type=variant_type,geno_missing_imputation=geno_missing_imputation,
 		                           Annotation_dir=Annotation_dir,Annotation_name_catalog=Annotation_name_catalog,Annotation_name=Annotation_name)
 	}
 	
 	if(category=="ptv_ds")
 	{
-		results <- info_synonymous(chr=chr,genofile=genofile,obj_nullmodel=obj_nullmodel,gene_name=gene_name,known_loci=known_loci,rare_maf_cutoff=rare_maf_cutoff,
+		results <- info_ptv_ds(chr=chr,genofile=genofile,obj_nullmodel=obj_nullmodel,gene_name=gene_name,known_loci=known_loci,rare_maf_cutoff=rare_maf_cutoff,
 		                           method_cond=method_cond,QC_label=QC_label,variant_type=variant_type,geno_missing_imputation=geno_missing_imputation,
 		                           Annotation_dir=Annotation_dir,Annotation_name_catalog=Annotation_name_catalog,Annotation_name=Annotation_name)
 	}
diff --git a/R/Gene_Centric_Coding_Results_Summary.R b/R/Gene_Centric_Coding_Results_Summary.R
index c640cde..d382955 100644
--- a/R/Gene_Centric_Coding_Results_Summary.R
+++ b/R/Gene_Centric_Coding_Results_Summary.R
@@ -166,6 +166,158 @@ Gene_Centric_Coding_Results_Summary <- function(agds_dir,gene_centric_coding_job
 	# synonymous
 	results_synonymous_genome <- results_synonymous_genome[results_synonymous_genome[,"cMAC"]>cMAC_cutoff,]
 
+	### recalculate missense pvalue
+	if(cMAC_cutoff > 0)
+	{
+		genes_name_disruptive_missense <- as.vector(unlist(results_disruptive_missense_genome[,1])) 
+		genes_name_missense <- as.vector(unlist(results_missense_genome[,1])) 
+
+		recal_id <- (1:dim(results_missense_genome)[1])[(!genes_name_missense%in%genes_name_disruptive_missense)]
+
+		for(kk in recal_id)
+		{
+			print(kk)
+			results_m <- results_missense_genome[kk,]
+			
+			if(use_SPA)
+			{
+				## disruptive missense cMAC < cut_off, set p-value to 1 
+				results_missense_genome[kk,"Burden(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"Burden(1,1)-Disruptive"] <- 1
+
+				apc_num <- (length(results_m)-10)/2
+				p_seq <- c(1:apc_num,1:apc_num+(apc_num+1))
+				
+				## calculate STAAR-B
+				pvalues_sub <- as.numeric(results_m[6:length(results_m)][p_seq])
+				
+				if(sum(is.na(pvalues_sub))>0)
+				{
+					if(sum(is.na(pvalues_sub))==length(pvalues_sub))
+					{
+						results_m["STAAR-B"] <- 1
+					}else
+					{
+						## not all NAs
+						pvalues_sub <- pvalues_sub[!is.na(pvalues_sub)]
+						if(sum(pvalues_sub[pvalues_sub<1])>0)
+						{
+							## not all ones
+							results_m["STAAR-B"] <- CCT(pvalues_sub[pvalues_sub<1])
+
+						}else
+						{
+							results_m["STAAR-B"] <- 1
+
+						}
+					}
+				}else
+				{
+					if(sum(pvalues_sub[pvalues_sub<1])>0)
+					{
+						results_m["STAAR-B"] <- CCT(pvalues_sub[pvalues_sub<1])
+					}else
+					{
+						results_m["STAAR-B"] <- 1
+					}
+				}
+				
+				results_missense_genome[kk,"STAAR-B"] <- results_m["STAAR-B"]
+				
+				## calculate STAAR-B(1,25)
+				pvalues_sub <- as.numeric(results_m[6:length(results_m)][c(1:apc_num)])
+				if(sum(is.na(pvalues_sub))>0)
+				{
+					if(sum(is.na(pvalues_sub))==length(pvalues_sub))
+					{
+						results_m["STAAR-B(1,25)"] <- 1
+					}else
+					{
+						## not all NAs
+						pvalues_sub <- pvalues_sub[!is.na(pvalues_sub)]
+						if(sum(pvalues_sub[pvalues_sub<1])>0)
+						{
+							## not all ones
+							results_m["STAAR-B(1,25)"] <- CCT(pvalues_sub[pvalues_sub<1])
+
+						}else
+						{
+							results_m["STAAR-B(1,25)"] <- 1
+
+						}
+					}
+				}else
+				{
+					if(sum(pvalues_sub[pvalues_sub<1])>0)
+					{
+						results_m["STAAR-B(1,25)"] <- CCT(pvalues_sub[pvalues_sub<1])
+					}else
+					{
+						results_m["STAAR-B(1,25)"] <- 1
+					}
+				}
+				
+				results_missense_genome[kk,"STAAR-B(1,25)"] <- results_m["STAAR-B(1,25)"]
+				
+				## calculate STAAR-B(1,1)
+				pvalues_sub <- as.numeric(results_m[6:length(results_m)][c(1:apc_num+(apc_num+1))])
+				if(sum(is.na(pvalues_sub))>0)
+				{
+					if(sum(is.na(pvalues_sub))==length(pvalues_sub))
+					{
+						results_m["STAAR-B(1,1)"] <- 1
+					}else
+					{
+						## not all NAs
+						pvalues_sub <- pvalues_sub[!is.na(pvalues_sub)]
+						if(sum(pvalues_sub[pvalues_sub<1])>0)
+						{
+							## not all ones
+							results_m["STAAR-B(1,1)"] <- CCT(pvalues_sub[pvalues_sub<1])
+
+						}else
+						{
+							results_m["STAAR-B(1,1)"] <- 1
+
+						}
+					}
+				}else
+				{
+					if(sum(pvalues_sub[pvalues_sub<1])>0)
+					{
+						results_m["STAAR-B(1,1)"] <- CCT(pvalues_sub[pvalues_sub<1])
+					}else
+					{
+						results_m["STAAR-B(1,1)"] <- 1
+					}
+				}
+				
+				results_missense_genome[kk,"STAAR-B(1,1)"] <- results_m["STAAR-B(1,1)"]
+			}else
+			{
+				## disruptive missense cMAC < cut_off, set p-value to 1 
+				results_missense_genome[kk,"Burden(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"Burden(1,1)-Disruptive"] <- 1
+				results_missense_genome[kk,"SKAT(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"SKAT(1,1)-Disruptive"] <- 1			
+				results_missense_genome[kk,"ACAT-V(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"ACAT-V(1,1)-Disruptive"] <- 1			
+				
+				apc_num <- (length(results_m)-19)/6
+				
+				p_seq <- c(1:apc_num,1:apc_num+(apc_num+1),1:apc_num+2*(apc_num+1),1:apc_num+3*(apc_num+1),1:apc_num+4*(apc_num+1),1:apc_num+5*(apc_num+1))
+
+				results_m["STAAR-O"] <- CCT(as.numeric(results_m[6:length(results_m)][p_seq]))
+				results_m["STAAR-S(1,25)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num)]))
+				results_m["STAAR-S(1,1)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+(apc_num+1))]))
+				results_m["STAAR-B(1,25)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+2*(apc_num+1))]))
+				results_m["STAAR-B(1,1)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+3*(apc_num+1))]))
+				results_m["STAAR-A(1,25)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+4*(apc_num+1))]))
+				results_m["STAAR-A(1,1)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+5*(apc_num+1))]))
+			}
+		}
+	}
+
 	###### whole-genome results
 	# plof
 	save(results_plof_genome,file=paste0(output_path,"plof.Rdata"))
diff --git a/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R b/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R
index e7095a0..32c399c 100644
--- a/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R
+++ b/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R
@@ -189,6 +189,160 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c
 	# ptv + disruptive missense
 	results_ptv_ds_genome <- results_ptv_ds_genome[results_ptv_ds_genome[,"cMAC"]>cMAC_cutoff,]
 
+
+	### recalculate missense pvalue
+	if(cMAC_cutoff > 0)
+	{
+		genes_name_disruptive_missense <- as.vector(unlist(results_disruptive_missense_genome[,1])) 
+		genes_name_missense <- as.vector(unlist(results_missense_genome[,1])) 
+
+		recal_id <- (1:dim(results_missense_genome)[1])[(!genes_name_missense%in%genes_name_disruptive_missense)]
+
+		for(kk in recal_id)
+		{
+			print(kk)
+			results_m <- results_missense_genome[kk,]
+			
+			if(use_SPA)
+			{
+				## disruptive missense cMAC < cut_off, set p-value to 1 
+				results_missense_genome[kk,"Burden(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"Burden(1,1)-Disruptive"] <- 1
+
+				apc_num <- (length(results_m)-10)/2
+				p_seq <- c(1:apc_num,1:apc_num+(apc_num+1))
+				
+				## calculate STAAR-B
+				pvalues_sub <- as.numeric(results_m[6:length(results_m)][p_seq])
+				
+				if(sum(is.na(pvalues_sub))>0)
+				{
+					if(sum(is.na(pvalues_sub))==length(pvalues_sub))
+					{
+						results_m["STAAR-B"] <- 1
+					}else
+					{
+						## not all NAs
+						pvalues_sub <- pvalues_sub[!is.na(pvalues_sub)]
+						if(sum(pvalues_sub[pvalues_sub<1])>0)
+						{
+							## not all ones
+							results_m["STAAR-B"] <- CCT(pvalues_sub[pvalues_sub<1])
+
+						}else
+						{
+							results_m["STAAR-B"] <- 1
+
+						}
+					}
+				}else
+				{
+					if(sum(pvalues_sub[pvalues_sub<1])>0)
+					{
+						results_m["STAAR-B"] <- CCT(pvalues_sub[pvalues_sub<1])
+					}else
+					{
+						results_m["STAAR-B"] <- 1
+					}
+				}
+				
+				results_missense_genome[kk,"STAAR-B"] <- results_m["STAAR-B"]
+				
+				## calculate STAAR-B(1,25)
+				pvalues_sub <- as.numeric(results_m[6:length(results_m)][c(1:apc_num)])
+				if(sum(is.na(pvalues_sub))>0)
+				{
+					if(sum(is.na(pvalues_sub))==length(pvalues_sub))
+					{
+						results_m["STAAR-B(1,25)"] <- 1
+					}else
+					{
+						## not all NAs
+						pvalues_sub <- pvalues_sub[!is.na(pvalues_sub)]
+						if(sum(pvalues_sub[pvalues_sub<1])>0)
+						{
+							## not all ones
+							results_m["STAAR-B(1,25)"] <- CCT(pvalues_sub[pvalues_sub<1])
+
+						}else
+						{
+							results_m["STAAR-B(1,25)"] <- 1
+
+						}
+					}
+				}else
+				{
+					if(sum(pvalues_sub[pvalues_sub<1])>0)
+					{
+						results_m["STAAR-B(1,25)"] <- CCT(pvalues_sub[pvalues_sub<1])
+					}else
+					{
+						results_m["STAAR-B(1,25)"] <- 1
+					}
+				}
+				
+				results_missense_genome[kk,"STAAR-B(1,25)"] <- results_m["STAAR-B(1,25)"]
+				
+				## calculate STAAR-B(1,1)
+				pvalues_sub <- as.numeric(results_m[6:length(results_m)][c(1:apc_num+(apc_num+1))])
+				if(sum(is.na(pvalues_sub))>0)
+				{
+					if(sum(is.na(pvalues_sub))==length(pvalues_sub))
+					{
+						results_m["STAAR-B(1,1)"] <- 1
+					}else
+					{
+						## not all NAs
+						pvalues_sub <- pvalues_sub[!is.na(pvalues_sub)]
+						if(sum(pvalues_sub[pvalues_sub<1])>0)
+						{
+							## not all ones
+							results_m["STAAR-B(1,1)"] <- CCT(pvalues_sub[pvalues_sub<1])
+
+						}else
+						{
+							results_m["STAAR-B(1,1)"] <- 1
+
+						}
+					}
+				}else
+				{
+					if(sum(pvalues_sub[pvalues_sub<1])>0)
+					{
+						results_m["STAAR-B(1,1)"] <- CCT(pvalues_sub[pvalues_sub<1])
+					}else
+					{
+						results_m["STAAR-B(1,1)"] <- 1
+					}
+				}
+				
+				results_missense_genome[kk,"STAAR-B(1,1)"] <- results_m["STAAR-B(1,1)"]
+			}else
+			{
+				## disruptive missense cMAC < cut_off, set p-value to 1 
+				results_missense_genome[kk,"Burden(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"Burden(1,1)-Disruptive"] <- 1
+				results_missense_genome[kk,"SKAT(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"SKAT(1,1)-Disruptive"] <- 1			
+				results_missense_genome[kk,"ACAT-V(1,25)-Disruptive"] <- 1
+				results_missense_genome[kk,"ACAT-V(1,1)-Disruptive"] <- 1			
+				
+				apc_num <- (length(results_m)-19)/6
+				
+				p_seq <- c(1:apc_num,1:apc_num+(apc_num+1),1:apc_num+2*(apc_num+1),1:apc_num+3*(apc_num+1),1:apc_num+4*(apc_num+1),1:apc_num+5*(apc_num+1))
+
+				results_m["STAAR-O"] <- CCT(as.numeric(results_m[6:length(results_m)][p_seq]))
+				results_m["STAAR-S(1,25)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num)]))
+				results_m["STAAR-S(1,1)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+(apc_num+1))]))
+				results_m["STAAR-B(1,25)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+2*(apc_num+1))]))
+				results_m["STAAR-B(1,1)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+3*(apc_num+1))]))
+				results_m["STAAR-A(1,25)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+4*(apc_num+1))]))
+				results_m["STAAR-A(1,1)"] <- CCT(as.numeric(results_m[6:length(results_m)][c(1:apc_num+5*(apc_num+1))]))
+			}
+		}
+	}
+
+
 	###### whole-genome results
 	# plof
 	save(results_plof_genome,file=paste0(output_path,"plof.Rdata"))
diff --git a/README.md b/README.md
index 2829c6c..699363d 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,4 @@
 [![R build status](https://github.com/xihaoli/STAARpipelineSummary/workflows/R-CMD-check/badge.svg)](https://github.com/xihaoli/STAARpipelineSummary/actions)
-[![Build status](https://ci.appveyor.com/api/projects/status/glc569adbr7ar11j/branch/main?svg=true)](https://ci.appveyor.com/project/xihaoli/staarpipelinesummary/branch/main)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 # STAARpipelineSummary
@@ -30,7 +29,7 @@ Please see the <a href="docs/STAARpipelineSummary_manual.pdf">**STAARpipelineSum
 ## Data Availability
 The whole-genome functional annotation data assembled from a variety of sources and the precomputed annotation principal components are available at the [Functional Annotation of Variant - Online Resource (FAVOR)](https://favor.genohub.org) site and [FAVOR Essential Database](https://doi.org/10.7910/DVN/1VGTJI).
 ## Version
-The current version is 0.9.7 (March 23, 2024).
+The current version is 0.9.7 (July 25, 2024).
 ## Citation
 If you use **STAARpipeline** and **STAARpipelineSummary** for your work, please cite: