BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238271.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,710,823 number of mapped reads = 2,486,576 (91.73%) number of supplementary alignments = 21,513 (0.79%) number of secondary alignments = 0 number of mapped bases = 162,949,449 bp number of sequenced bases = 162,860,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,310 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9234 >>>>>>> ACTG content number of A's = 44,761,317 bp (27.48%) number of C's = 30,706,034 bp (18.85%) number of T's = 50,075,000 bp (30.75%) number of G's = 37,272,714 bp (22.89%) number of N's = 44,957 bp (0.03%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,431,698 number of insertions = 13,157 mapped reads with insertion percentage = 0.52% number of deletions = 54,176 mapped reads with deletion percentage = 2.15% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.0526X std coverageData = 0.4507X There is a 4.42% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17678028 0.07092470995287911 0.8971343761962645 chr2 243199373 11849116 0.04872181968988876 0.5273437210076782 chr3 198022430 9910094 0.05004531052366139 0.25841153103783676 chr4 191154276 9197102 0.04811350387997598 0.2854586699948839 chr5 180915260 12722216 0.07032140903979023 0.30571511242751376 chr6 171115067 10866119 0.06350182476917711 0.3556613906783814 chr7 159138663 7940480 0.04989661123394005 0.5804433685599787 chr8 146364022 8639554 0.05902785317009121 0.5187690707332464 chr9 141213431 5923566 0.04194761049322568 0.36253903900027196 chr10 135534747 7518362 0.05547184147545574 0.4972778946767369 chr11 135006516 6643253 0.04920690642813122 0.3281947291938696 chr12 133851895 7644364 0.05711061468349029 0.28161559624153615 chr13 115169878 3875726 0.03365225410762352 0.21037953833394912 chr14 107349540 4182424 0.03896080039094718 0.27180170302907636 chr15 102531392 3300955 0.032194579002692174 0.21335559314674657 chr16 90354753 4203807 0.04652557680059177 0.29246153578889256 chr17 81195210 3896037 0.04798358179010806 0.2866010247214455 chr18 78077248 4947580 0.0633677559946785 0.6749433498402199 chr19 59128983 2633661 0.04454094872560213 0.6173527525895599 chr20 63025520 3246137 0.05150512046548763 0.26940243011401366 chr21 48129895 2326942 0.04834712396526109 0.27995465370179734 chr22 51304566 2037463 0.039713092982796114 0.22871075096058727 chrMT 16571 5520 0.3331120632430149 0.7313985295396932 chrX 155270560 11275322 0.07261725596919338 0.34954633263221846 chrY 59373566 485621 0.008179077537636867 0.19583321588481084