BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237828.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 = 2,981,520 number of mapped reads = 2,657,009 (89.12%) number of supplementary alignments = 33,872 (1.14%) number of secondary alignments = 0 number of mapped bases = 180,773,419 bp number of sequenced bases = 180,640,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 519,874 duplication rate = 13.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8086 >>>>>>> ACTG content number of A's = 52,683,366 bp (29.16%) number of C's = 33,378,931 bp (18.48%) number of T's = 56,788,543 bp (31.44%) number of G's = 37,496,799 bp (20.76%) number of N's = 292,947 bp (0.16%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,720,791 number of insertions = 14,695 mapped reads with insertion percentage = 0.55% number of deletions = 75,284 mapped reads with deletion percentage = 2.78% homopolymer indels = 43.13% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.96X There is a 1.47% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 19527903 0.07834645675767443 1.8056940997728783 chr2 243199373 14074643 0.05787285890741174 0.8686707441512797 chr3 198022430 12347480 0.06235394646959943 0.7735650877593375 chr4 191154276 11668287 0.06104120317978134 0.7969756495138168 chr5 180915260 10188148 0.05631447562798185 0.7299959690003145 chr6 171115067 6489010 0.03792190900407385 0.6291457050348771 chr7 159138663 12690505 0.07974495173432493 0.9874557643344931 chr8 146364022 6594630 0.04505635954715702 1.4291221515970225 chr9 141213431 9481920 0.06714602097586596 0.8322665303781772 chr10 135534747 5585375 0.041209912023519694 0.9049675871230247 chr11 135006516 9919040 0.07347082417859002 0.8425060187246067 chr12 133851895 8086485 0.06041367587660974 0.7523352404045727 chr13 115169878 8213777 0.07131879570107733 0.8164053247670187 chr14 107349540 5412539 0.050419768915637646 0.7148456056307388 chr15 102531392 4721316 0.04604751684245153 0.6748190336149572 chr16 90354753 5013878 0.05549102657610054 0.7316761370692664 chr17 81195210 3832757 0.04720422547093603 0.7130674870846236 chr18 78077248 3181540 0.04074861859885225 0.9263569989713806 chr19 59128983 3287805 0.05560394975844587 1.2002334524009801 chr20 63025520 3786640 0.06008105922807142 0.7531813319183374 chr21 48129895 2473182 0.05138556815883351 0.7210076354566708 chr22 51304566 1071228 0.020879779004465217 0.4398496528316905 chrMT 16571 32716 1.97429243859755 3.997024485234122 chrX 155270560 12386029 0.07977062103723977 0.8599231079770407 chrY 59373566 706586 0.011900683209763752 0.4407406448986186