update usage

Author: ilight1542

docs/usage.md

@@ -102,7 +102,7 @@ Only the `reference_name`, and `fasta` columns are mandatory, whereas all other
 | pmdtools_bed_for_masking    | No       | Optional path to SNP capture BED file to mask the reference for PMDtools                                                   |
 | sexdeterrmine_snp_bed       | No       | Optional path to SNP capture bed files for genetic sex estimation with SexDetERRmine                                       |
 | bedtools_feature_file       | No       | Optional path to feature file for coverage calculation with bedtools                                                       |
-| genotyping_reference_ploidy | No       | Optional integer to specify organism ploidy for genotyping with GATK or FreeBayes                                          |
+| genotyping_reference_ploidy | No       | Optional integer to specify organism ploidy for genotyping with GATK or FreeBayes (by default set to 2)                    |
 | genotyping_gatk_dbsnp       | No       | Optional path to SNP annotation file for genotyping with GATK                                                              |
 
 Files for `fai`, `dict`, `mapper_index` will be generated by the pipeline for you if not specified.