BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236072.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 = 1,704,526 number of mapped reads = 1,336,148 (78.39%) number of supplementary alignments = 9,164 (0.54%) number of secondary alignments = 0 number of mapped bases = 87,602,242 bp number of sequenced bases = 87,558,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,533 duplication rate = 6.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4568 >>>>>>> ACTG content number of A's = 23,804,770 bp (27.19%) number of C's = 15,398,033 bp (17.59%) number of T's = 28,707,098 bp (32.79%) number of G's = 19,598,455 bp (22.38%) number of N's = 50,643 bp (0.06%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 708,733 number of insertions = 6,175 mapped reads with insertion percentage = 0.46% number of deletions = 24,805 mapped reads with deletion percentage = 1.84% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.3107X There is a 2.05% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 10969634 0.044010458052178736 0.5954376123671464 chr2 243199373 4919750 0.020229287350999874 0.28027064103408184 chr3 198022430 6106575 0.030837794486210476 0.23635851972844388 chr4 191154276 3136696 0.016409237949769954 0.1716478409751334 chr5 180915260 6580499 0.03637337723749782 0.2531296724615302 chr6 171115067 7867251 0.045976377988970425 0.29977688576238903 chr7 159138663 3517984 0.022106406662471458 0.22152858009416643 chr8 146364022 5290778 0.03614807742848171 0.632097971126841 chr9 141213431 4660865 0.03300581939688159 0.2629219640240472 chr10 135534747 5092546 0.03757373007823595 0.27706928743965203 chr11 135006516 1402302 0.010386920880174406 0.1510087629495678 chr12 133851895 2965830 0.02215754958119943 0.19804423473932148 chr13 115169878 5230405 0.0454146960197353 0.28292660478782466 chr14 107349540 2033756 0.018945176663076525 0.18500983640578925 chr15 102531392 2510069 0.02448098042012343 0.2083357828149405 chr16 90354753 2710442 0.02999777997290303 0.22653936124586843 chr17 81195210 2353868 0.02899023230557566 0.21904982324209538 chr18 78077248 1493582 0.01912954206582691 0.30860093237493036 chr19 59128983 2747272 0.04646235840044805 0.38223798534220776 chr20 63025520 1083965 0.017198826760969208 0.17277141359584977 chr21 48129895 1078470 0.02240748707222403 0.19638080401598673 chr22 51304566 973607 0.01897700489270292 0.1781380838822766 chrMT 16571 20873 1.2596101623317844 1.6197641849792712 chrX 155270560 2701332 0.017397580069267476 0.1769769183213127 chrY 59373566 153891 0.0025919110197962507 0.06821299969831592