gencore report

Summary

General

gencore version:	0.12.0 (https://github.com/OpenGene/gencore)
mapping rate:	0.997838
duplication rate:	0.401911
fragment passing rate:	1.000000

Details

	before processing	after processing
total bases:	2.814956 G	1.661835 G
mapped bases:	2.810305 G	1.657184 G
total reads:	23.350246 M	13.979907 M
mapped reads:	23.299758 M	13.929419 M
mismatched bases:	6.396757 M	2.466189 M
reads with mismatched bases:	6.396757 M	2.466189 M
mismatch rate:	0.002276	0.001488
total mapping clusters:	7.026346 M	7.026346 M
multiple fragments clusters:	0	0
total fragments:	7.026346 M	7.026346 M
single-end fragments:	117.358000 K	121.349000 K
paired-end fragments:	6.908988 M	6.904997 M

Duplication histogram of mapped reads

Coverage statistics in genome scale

Before processing

After processing

Coverage statistics in BED:/Users/shifu/data/bed/test.bed

Before processing

After processing

./gencore -i /Users/shifu/data/bam/input.sorted.bam -o output.bam -r /Users/shifu/data/ref/hg19.fa -b /Users/shifu/data/bed/test.bed --coverage_sampling=50000