diff --git a/data/test.gff b/data/test.gff
index ee33aabc..9a5f0d9f 100644
--- a/data/test.gff
+++ b/data/test.gff
@@ -1,7 +1,7 @@
 ## GFF3 file format
-test	Genbank	primer_binding_site	2	290	.	+	.	ID=id-test1;Note=daft punk
-test	Genbank	long_terminal_repeat	1	55	.	+	.	ID=id-test2;Note=random access memories
-test	Genbank	CDS	2	292	.	+	.	ID=id-test3;Note=eluvite
-test	Genbank	CDS	1	55	.	+	.	ID=id-test4;Note=ategnato
-test	Genbank	CDS	2	292	.	+	.	ID=id-testedit1;Note=PinkFloyd;EditPosition=100;EditSequence=A
-test	Genbank	CDS	2	292	.	+	.	ID=id-testedit2;Note=AnotherBrickInTheWall;EditPosition=102;EditSequence=AA
\ No newline at end of file
+test	Genbank	primer_binding_site	2	290	.	+	.	ID=id-test1;Note=daft punk;Parent=geneFragmentsOfTime;
+test	Genbank	long_terminal_repeat	1	55	.	+	.	ID=id-test2;Note=random access memories;Parent=geneGetLucky;
+test	Genbank	CDS	2	292	.	+	.	ID=id-test3;Note=eluvite;gene=geneKatyPerry;
+test	Genbank	CDS	1	55	.	+	.	ID=id-test4;Note=ategnato;gene=geneKatyPerry;
+test	Genbank	CDS	2	292	.	+	.	ID=id-testedit1;Note=PinkFloyd;EditPosition=100;EditSequence=A;
+test	Genbank	CDS	2	292	.	+	.	ID=id-testedit2;Note=AnotherBrickInTheWall;EditPosition=102;EditSequence=AA;gene=geneTaylorSwift;
diff --git a/src/call_variants.cpp b/src/call_variants.cpp
index 46d10555..4f7ab4d6 100644
--- a/src/call_variants.cpp
+++ b/src/call_variants.cpp
@@ -28,6 +28,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
   ref_antd refantd(ref_path, gff_path);
   std::ostringstream out_str;
   std::ofstream fout((out_file+".tsv").c_str());
+  //make columns in the file
   fout << "REGION"
     "\tPOS"
     "\tREF"
@@ -47,6 +48,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
     "\tREF_AA"
     "\tALT_CODON"
     "\tALT_AA"
+    "\tPOS_AA"
        << std::endl;
   int ctr = 0;
   int64_t pos = 0;
@@ -118,6 +120,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
       freq_depth = get_frequency_depth(*it, pdepth, mdepth);
       if(freq_depth[0] < min_threshold)
 	continue;
+      //this only adds the first bit of the information to the tsv
       out_str << region << "\t";
       out_str << pos << "\t";
       out_str << ref << "\t";
@@ -135,6 +138,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
 	Exp | Error | Err free |
 	Obs | AD    | RD       |
        */
+      //adding pvalue related info
       err = pow(10, ( -1 * (it->mean_qual)/10));
       kt_fisher_exact((err * mdepth), (1-err) * mdepth, it->depth, ref_it->depth, &pval_left, &pval_right, &pval_twotailed);
       out_str << pval_left << "\t";
@@ -143,10 +147,11 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
       } else {
 	out_str << "FALSE" << "\t";
       }
+      //adding codon related info, can add gene info here too
       if(it->nuc[0] != '+' && it->nuc[0] != '-'){
 	refantd.codon_aa_stream(region, out_str, fout, pos, it->nuc[0]);
       } else {
-	fout << out_str.str() << "NA\tNA\tNA\tNA\tNA" << std::endl;
+	fout << out_str.str() << "NA\tNA\tNA\tNA\tNA\tNA" << std::endl;
       }
       out_str.str("");
       out_str.clear();
diff --git a/src/ref_seq.cpp b/src/ref_seq.cpp
index 1b3d22a4..d52ef05c 100644
--- a/src/ref_seq.cpp
+++ b/src/ref_seq.cpp
@@ -109,23 +109,35 @@ ref_antd::~ref_antd()
   if (this->fai) fai_destroy(this->fai);
 }
 
+//used to add codon info to variants output
 int ref_antd::codon_aa_stream(std::string region, std::ostringstream &line_stream, std::ofstream &fout, int64_t pos, char alt){
   std::vector<gff3_feature> features = gff.query_features(pos, "CDS");
   if(features.size() == 0){	// No matching CDS
-    fout << line_stream.str() << "NA\tNA\tNA\tNA\tNA" << std::endl;
+    fout << line_stream.str() << "NA\tNA\tNA\tNA\tNA\tNA" << std::endl;
     return 0;
   }
   std::vector<gff3_feature>::iterator it;
   char *ref_codon, *alt_codon;
   for(it = features.begin(); it != features.end(); it++){
     fout << line_stream.str();
-    fout << it->get_attribute("ID") << "\t";
+    //add in gene level info, control for case it's not present
+    std::string gene = it->get_attribute("gene");
+    if (gene.empty()){
+        fout << it->get_attribute("ID") << "\t";
+    } else {
+        fout << gene + ":" + it->get_attribute("ID") << "\t";
+    }
     ref_codon = this->get_codon(pos, region, *it);
     fout << ref_codon[0] << ref_codon[1] << ref_codon[2] << "\t";
     fout << codon2aa(ref_codon[0], ref_codon[1], ref_codon[2]) << "\t";
     alt_codon = this->get_codon(pos, region, *it, alt);
     fout << alt_codon[0] << alt_codon[1] << alt_codon[2] << "\t";
-    fout << codon2aa(alt_codon[0], alt_codon[1], alt_codon[2]);
+    fout << codon2aa(alt_codon[0], alt_codon[1], alt_codon[2]) << "\t";
+    
+    //adding amino acid position
+    int64_t start = it->get_start();
+    int64_t aa_pos = ((pos - start) / 3)+1;
+    fout << aa_pos;
     fout << std::endl;
 
     delete[] ref_codon;
diff --git a/tests/test_variants.cpp b/tests/test_variants.cpp
index 4d21f01c..d7d42dc4 100755
--- a/tests/test_variants.cpp
+++ b/tests/test_variants.cpp
@@ -12,11 +12,13 @@ int call_var_check_outfile(std::string prefix, uint8_t min_qual, uint8_t min_dep
   std::string l;
   getline(outFile, l);		// Ignore first line
   int comp = 0, ctr = 0;
+  
   while(ctr < len){
     getline(outFile, l);
     std::cout << l << std::endl;
     std::cout << out[ctr] << " -> CORRECT" << std::endl;
     comp += l.compare(out[ctr]);
+    std::cout << l.compare(out[ctr]) << "\n"; 
     ctr++;
   }
   return comp;
@@ -25,20 +27,20 @@ int call_var_check_outfile(std::string prefix, uint8_t min_qual, uint8_t min_dep
 int main() {
   int num_success = 0;
   // Quality threshold 20. Frequency threshold: 0.03. Total_DP = 3. Indel passes filters with total_depth 4. Has two lines.
-  std::string t_20_02_1[4] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*", "test\t210\tA\t+GT\t1\t1\t41\t1\t0\t20\t0.25\t4\t0.4\tFALSE\tNA\tNA\tNA\tNA\tNA"};
+  std::string t_20_02_1[4] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70", "test\t210\tA\t+GT\t1\t1\t41\t1\t0\t20\t0.25\t4\t0.4\tFALSE\tNA\tNA\tNA\tNA\tNA\tNA"};
   // Quality threshold 3-. Frequency threshold: 0.03. Total_DP = 3. Freq = 0.666667 No Indel
-  std::string t_20_03[3] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*"};
+  std::string t_20_03[3] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70"};
   // Quality threshold 25. Frequency threshold: 0.03. Total_DP = 2. Freq = 0.5 No Indel.
-  std::string t_25_03[3] = {"test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*"};
+  std::string t_25_03[3] = {"test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70"};
   // Minimum depth threshold. Should be empty
   std::string t_25_03_20[] = {};
   num_success = call_var_check_outfile("../data/test.indel", 20, 0, 0.02, t_20_02_1, 4);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 20, 0, 0.03, t_20_03, 3);
+  num_success += call_var_check_outfile("../data/test.indel2", 20, 0, 0.03, t_20_03, 3);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 25, 0, 0.03, t_25_03, 3);
+  num_success += call_var_check_outfile("../data/test.indel3", 25, 0, 0.03, t_25_03, 3);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 25, 20, 0.03, t_25_03_20, 0);
+  num_success += call_var_check_outfile("../data/test.indel4", 25, 20, 0.03, t_25_03_20, 0);
   std::cout << num_success << std::endl;
   if(num_success == 0)
     return 0;