BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926920.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 23,155,932 number of mapped reads = 21,485,426 (92.79%) number of supplementary alignments = 245,445 (1.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,818,150 number of mapped paired reads (second in pair) = 10,667,276 number of mapped paired reads (both in pair) = 21,179,808 number of mapped paired reads (singletons) = 305,618 number of mapped bases = 2,029,993,604 bp number of sequenced bases = 2,028,416,885 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,308,386 duplication rate = 4.98% >>>>>>> Insert size mean insert size = 116,533.6 std insert size = 3,346,434.5436 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.3538 >>>>>>> ACTG content number of A's = 581,479,583 bp (28.67%) number of C's = 406,688,138 bp (20.05%) number of T's = 586,349,693 bp (28.91%) number of G's = 453,704,239 bp (22.37%) number of N's = 195,232 bp (0.01%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 20,873,625 number of insertions = 329,436 mapped reads with insertion percentage = 1.51% number of deletions = 1,114,873 mapped reads with deletion percentage = 5.05% homopolymer indels = 53.04% >>>>>>> Coverage mean coverageData = 0.6557X std coverageData = 2.6171X There is a 28.11% of reference with a coverageData >= 1X There is a 14.84% of reference with a coverageData >= 2X There is a 8.21% of reference with a coverageData >= 3X There is a 4.88% of reference with a coverageData >= 4X There is a 3% of reference with a coverageData >= 5X There is a 1.9% of reference with a coverageData >= 6X There is a 1.23% of reference with a coverageData >= 7X There is a 0.81% of reference with a coverageData >= 8X There is a 0.54% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% 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 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 166713039 0.6688570657563176 2.2886875048446162 chr2 243199373 170077466 0.699333488824414 2.9879729154542516 chr3 198022430 138994267 0.7019117329284364 1.562636806425945 chr4 191154276 121834329 0.6373612536922795 1.585965422326495 chr5 180915260 123398982 0.6820816663005652 1.4803913076229616 chr6 171115067 116469057 0.680647584353282 1.779123849377374 chr7 159138663 100292103 0.6302183335548068 1.6407073976976234 chr8 146364022 101847019 0.6958473647301111 1.5862848248271475 chr9 141213431 83901171 0.5941444125098837 2.472325292277968 chr10 135534747 101172624 0.7464700103804377 8.402671289342296 chr11 135006516 97175393 0.7197829844005456 1.8367778471277547 chr12 133851895 90361097 0.6750826874733451 1.5950158781397925 chr13 115169878 58112616 0.5045817275242751 1.2998940481037402 chr14 107349540 58097503 0.5411993661081361 1.3685562432353502 chr15 102531392 60052155 0.5856953058825145 1.483366648208585 chr16 90354753 63105188 0.6984158099574463 3.4423556512386337 chr17 81195210 53782192 0.6623813399829866 1.669342822669512 chr18 78077248 52725086 0.6752938576933449 2.693932543228215 chr19 59128983 32110764 0.5430630186891596 1.6683933521008631 chr20 63025520 48416491 0.768204546348844 1.745941549595336 chr21 48129895 47733705 0.9917683177991558 2.623051413365815 chr22 51304566 26739261 0.5211867692244 1.435239730860035 chrMT 16571 74587 4.501056061794702 3.5400140746814137 chrX 155270560 113898003 0.7335453868395915 1.651956149282279 chrY 59373566 2909506 0.04900338982502752 0.977267278458798