Figure 1 | Scientific Reports

Figure 1

From: An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

Figure 1

Pipeline showing the number of variants involved in the different steps. SNPs hard-filtering criteria: QualByDepth (QD) < 10.0, Quality (QUAL) < 30.0, StrandOddsRatio (SOR) > 3.0, FisherStrand (FS) > 60.0, RMSMappingQuality (MQ) < 40.0, MappingQualityRankSumTest (MQRankSum) < -12.5 and ReadPosRankSumTest (ReadPosRankSum) < -8.0. Indels hard-filtering criteria: QualByDepth (QD) < 2.0, Quality (QUAL) < 30.0, FisherStrand (FS) > 200.0 and ReadPosRankSumTest (ReadPosRankSum) < -20.0.

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