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Take a look at the resulting file: 61FTVAAXX.ab.sam.links.filtered.sv.txt
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We've highlighted a few lines below:
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chr_type SV_type BAL_type chromosome1 start1-end1 average_dist chromosome2 start2-end2 nb_pairs score_strand_filtering score_order_filtering score_insert_size_filtering final_score breakpoint1_start1-end1 breakpoint2_start2-end2 ... INTRA NORMAL_SENSE - chrNC_012967 599566-601025 - chrNC_012967 663036-664898 430 100% - - 1 - - ... INTRA NORMAL_SENSE - chrNC_012967 3-2025 - chrNC_012967 4627019-4628998 288 100% - - 1 - - ... INTRA REVERSE_SENSE - chrNC_012967 16999-19033 - chrNC_012967 2775082-2777014 274 100% - - 1 - - |
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1. This is a tandem head-to-tail duplication of the region from approximately 600000 to 663000. ... Many of the others are due to new insertions of transposable elements. |
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