BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230351.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 = 2,560,928 number of mapped reads = 1,932,627 (75.47%) number of supplementary alignments = 8,725 (0.34%) number of secondary alignments = 0 number of mapped bases = 125,256,164 bp number of sequenced bases = 125,207,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,590 duplication rate = 3.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0801 >>>>>>> ACTG content number of A's = 33,504,156 bp (26.76%) number of C's = 21,383,022 bp (17.08%) number of T's = 41,950,864 bp (33.51%) number of G's = 28,138,660 bp (22.47%) number of N's = 230,542 bp (0.18%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,140,848 number of insertions = 11,088 mapped reads with insertion percentage = 0.57% number of deletions = 30,023 mapped reads with deletion percentage = 1.54% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.3502X There is a 3.41% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% 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 8928317 0.03582064094436098 0.4285246973849941 chr2 243199373 10937894 0.04497500904330045 0.38331632209517075 chr3 198022430 10808009 0.05457972109523149 0.2694190479993047 chr4 191154276 6853626 0.03585389845006658 0.24007205581270075 chr5 180915260 6594075 0.036448417894654105 0.21862132062018064 chr6 171115067 9712435 0.05675967154897003 0.34151755938089 chr7 159138663 10284189 0.06462407567166754 0.665255674315483 chr8 146364022 4839229 0.03306296816576959 0.45271886418640167 chr9 141213431 5634101 0.03989777006409539 0.3609705781884633 chr10 135534747 8645229 0.06378607103608641 0.38612143822327355 chr11 135006516 1966624 0.014566882090342959 0.17809086836520518 chr12 133851895 6747992 0.05041386974760424 0.26566751061425825 chr13 115169878 2038809 0.017702623597465304 0.15353648764548675 chr14 107349540 2956472 0.027540611725024627 0.20694071496364058 chr15 102531392 4169184 0.040662512413759094 0.23046353940793932 chr16 90354753 2261864 0.025033149058578025 0.21104302455416307 chr17 81195210 2707498 0.03334553848681468 0.21194048942770824 chr18 78077248 3190313 0.04086098167804275 0.5910046665499846 chr19 59128983 2179897 0.03686681030857575 0.32867754700928126 chr20 63025520 2687403 0.04263991792531026 0.2492986458451583 chr21 48129895 1856201 0.038566487626868914 0.2587328724617028 chr22 51304566 1299339 0.025325991452690585 0.19027829737502294 chrMT 16571 399457 24.105787218634966 18.312847671207646 chrX 155270560 7236430 0.04660529336662404 0.2736039250780651 chrY 59373566 321577 0.005416164493134874 0.12872459553944254