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--- tutorials:population-diversity:snp-chips [2020/09/22 09:14] – [Data analysis workflow with Plink 1.9] bngina
+++ tutorials:population-diversity:snp-chips [2020/09/22 10:09] – [Data analysis workflow with Plink 1.9] bngina
@@ Line 183: / Line 183: @@
   *//bin_caprin_60k.lmiss// - for the loci
-<code>
-#The missing information found in the ''bin_caprin_60k.imiss'' for the individuals looks like below;
+#The missing information found in the ''bin_caprin_60k.imiss'' for the individuals looks like below;
+<code>
 FID                               IID MISS_PHENO   N_MISS   N_GENO   F_MISS
           WG6694108-DNA_A01_110kin          Y     1325    53347  0.02484
@@ Line 199: / Line 199: @@
            WG6694108-DNA_A10_Zkin2          Y     1349    53347  0.02529
-##the information in each header is as follows;
+</code>
+The information in each header is as follows;
+<code>
 FID                Family ID
 IID                Individual ID
@@ Line 207: / Line 209: @@
 N_GENO             Number of non-obligatory missing genotypes i.e total number of SNPs used
 F_MISS             Proportion of missing SNPs (in percentage)
+</code>
+The information found in the ''bin_caprin_60k.lmiss'' for the SNPs is as below;
-#The information found in the ''bin_caprin_60k.lmiss'' for the SNPs is as below;
+<code>
  CHR                           SNP   N_MISS   N_GENO   F_MISS
            snp1-scaffold1-2170        4      648 0.006173
@@ Line 222: / Line 224: @@
   snp10004-scaffold1356-853276        3      648  0.00463
   snp10005-scaffold1356-907019        2      648 0.003086
+</code>
-#The information in each column is as follows;
+The information in each column is as follows;
+<code>
 SNP                SNP identifier
 CHR                Chromosome number
@@ Line 230: / Line 233: @@
 N_GENO             Number of non-obligatory missing genotypes i.e total number of genotypes in the population
 F_MISS             Proportion of sample missing for this SNP (in percentage)
 </code>
+We can generate a file with filters added for the rate missing data in individuals ''--mind'' and call rate for the SNPs ''--geno'' and also for the minor allele frequency //(MAF)// .
 ===== Data analysis workflow with R and adegenet =====