BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008783.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 = 1,312,099 number of mapped reads = 1,148,500 (87.53%) number of supplementary alignments = 12,841 (0.98%) number of secondary alignments = 0 number of mapped bases = 75,459,164 bp number of sequenced bases = 75,419,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,921 duplication rate = 8.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8427 >>>>>>> ACTG content number of A's = 20,352,560 bp (26.99%) number of C's = 14,599,496 bp (19.36%) number of T's = 23,184,956 bp (30.74%) number of G's = 17,173,354 bp (22.77%) number of N's = 109,217 bp (0.14%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 661,296 number of insertions = 5,626 mapped reads with insertion percentage = 0.48% number of deletions = 22,192 mapped reads with deletion percentage = 1.91% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.3298X There is a 1.4% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 9426681 0.03782009032587325 0.564541263086346 chr2 243199373 7508321 0.030873110022368356 0.43510126717733383 chr3 198022430 4553281 0.022993763888262558 0.2414125349237721 chr4 191154276 4765863 0.024932024016036135 0.2519040115906943 chr5 180915260 5094473 0.02815944326642208 0.2673045563430838 chr6 171115067 3829490 0.022379618973003702 0.25698715523018256 chr7 159138663 3327282 0.02090806807896834 0.30148350157088766 chr8 146364022 5713235 0.03903442199750428 0.4600268090544686 chr9 141213431 1074041 0.007605799196253506 0.1945796879495189 chr10 135534747 6368089 0.04698491819223302 0.4386283776072255 chr11 135006516 2032472 0.015054621511749848 0.2096606758858336 chr12 133851895 2563804 0.019154035884213667 0.21839757597227646 chr13 115169878 1685411 0.014634130288824305 0.19380481071881148 chr14 107349540 1829700 0.017044320823358907 0.21225136441796502 chr15 102531392 1635988 0.0159559718061762 0.19889181671264888 chr16 90354753 1848609 0.020459454966359102 0.27123537667799824 chr17 81195210 2741338 0.03376231184080933 0.3126436770156314 chr18 78077248 1043507 0.013365058666002162 0.3949175157393653 chr19 59128983 1175040 0.019872487913414644 0.41121123721566605 chr20 63025520 2372160 0.03763808692098058 0.3225667325758741 chr21 48129895 822164 0.01708218976999638 0.20893558641682486 chr22 51304566 1491748 0.02907632041951198 0.27715327341751705 chrMT 16571 240473 14.511677026129986 10.540183950978712 chrX 155270560 2158287 0.013900168840764147 0.18688530200646322 chrY 59373566 157707 0.002656182045727218 0.09696701127539825