BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238302.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 = 1,631,993 number of mapped reads = 1,487,305 (91.13%) number of supplementary alignments = 18,774 (1.15%) number of secondary alignments = 0 number of mapped bases = 97,993,223 bp number of sequenced bases = 97,946,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,358 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3637 >>>>>>> ACTG content number of A's = 27,132,266 bp (27.7%) number of C's = 17,591,306 bp (17.96%) number of T's = 31,507,017 bp (32.17%) number of G's = 21,637,910 bp (22.09%) number of N's = 77,591 bp (0.08%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 797,273 number of insertions = 7,268 mapped reads with insertion percentage = 0.49% number of deletions = 26,972 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.3271X There is a 2.61% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% 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% 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 7727596 0.031003316938576456 0.5182867278124771 chr2 243199373 8285413 0.034068397865482984 0.36861157715465503 chr3 198022430 4995754 0.02522822288364 0.18440886015446978 chr4 191154276 4988996 0.026099316763387496 0.21259652053270775 chr5 180915260 5303276 0.029313591346578502 0.20242130050692814 chr6 171115067 6903680 0.0403452490831798 0.2830377895827545 chr7 159138663 5820135 0.03657272777263436 0.433189195412118 chr8 146364022 5502895 0.037597320193893 0.5729212348307843 chr9 141213431 4400668 0.031163239706285446 0.3057288020070307 chr10 135534747 5307426 0.039159153777739375 0.3207535801882903 chr11 135006516 5137857 0.038056363146205474 0.2988291162283634 chr12 133851895 4679278 0.03495862348456105 0.22336898720873677 chr13 115169878 3237650 0.02811195128642925 0.19608011271274425 chr14 107349540 2973478 0.027699028798819258 0.21351340152483117 chr15 102531392 2978196 0.029046674797899946 0.2014896890391647 chr16 90354753 2264543 0.02506279885464354 0.2038508023541236 chr17 81195210 2577406 0.0317433257454473 0.2355445099820966 chr18 78077248 2885636 0.036958730922483335 0.5617346053297224 chr19 59128983 1416985 0.023964305288321972 0.3357098674938423 chr20 63025520 1970542 0.03126577932240781 0.21328283830569847 chr21 48129895 1272935 0.026447907272600532 0.20923737921254096 chr22 51304566 1019218 0.0198660290781916 0.16078839464618203 chrMT 16571 3156 0.19045320137589766 0.4523608736994955 chrX 155270560 6078277 0.03914635845971059 0.2598636797119097 chrY 59373566 262227 0.0044165614037735244 0.12806921530217805