BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524498.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,750,866 number of mapped reads = 2,539,383 (92.31%) number of supplementary alignments = 5,629 (0.2%) number of secondary alignments = 0 number of mapped bases = 147,669,744 bp number of sequenced bases = 147,622,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 157,178 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3131 >>>>>>> ACTG content number of A's = 36,464,078 bp (24.7%) number of C's = 26,242,336 bp (17.78%) number of T's = 46,052,581 bp (31.2%) number of G's = 38,860,171 bp (26.32%) number of N's = 2,963 bp (0%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 697,045 number of insertions = 9,133 mapped reads with insertion percentage = 0.36% number of deletions = 27,849 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.4033X There is a 3.97% of reference with a coverageData >= 1X There is a 0.56% 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 14501442 0.05818016397238986 0.7232338287536665 chr2 243199373 11520308 0.04736980962529044 0.4749475370017312 chr3 198022430 9083827 0.04587271755022903 0.2505415341501882 chr4 191154276 8336431 0.043611009779347024 0.286921278536895 chr5 180915260 8038861 0.044434399840013496 0.24725120664957362 chr6 171115067 6352716 0.03712540404171422 0.3233336817680672 chr7 159138663 6379607 0.040088353639115344 0.5582511688917383 chr8 146364022 13595794 0.09289027326674584 0.4315633169443653 chr9 141213431 6319716 0.04475293855015816 0.35288428858803267 chr10 135534747 7728227 0.057020263593364734 0.4121056146852945 chr11 135006516 5051016 0.037413127526378064 0.3859035501032801 chr12 133851895 6889374 0.05147012673970735 0.2681419658021771 chr13 115169878 3242017 0.028149869187149786 0.1985218533140502 chr14 107349540 3503883 0.03263994424195949 0.21881269522384 chr15 102531392 3921232 0.03824420914913552 0.2414020115241687 chr16 90354753 4697767 0.051992472382720145 0.29581308888854446 chr17 81195210 5194169 0.06397137220286764 0.31907737017142634 chr18 78077248 3483954 0.04462188523857808 0.6404872203767408 chr19 59128983 3014687 0.050984928998356015 0.5642953346644575 chr20 63025520 4259693 0.06758679658652558 0.31281259626579233 chr21 48129895 2030828 0.04219473156964086 0.26974045881895686 chr22 51304566 1202943 0.023447094358034333 0.1785541829476451 chrMT 16571 16918 1.0209401967292258 1.314925339915742 chrX 155270560 8826872 0.05684832977996602 0.3274359423247375 chrY 59373566 477462 0.00804165948193174 0.213212689704263