BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504411.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 149,364,512 number of mapped reads = 148,630,318 (99.51%) number of supplementary alignments = 2,529,791 (1.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 74,407,437 number of mapped paired reads (second in pair) = 74,222,881 number of mapped paired reads (both in pair) = 148,249,132 number of mapped paired reads (singletons) = 381,186 number of mapped bases = 14,216,028,222 bp number of sequenced bases = 14,211,471,060 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,231,320 duplication rate = 28.36% >>>>>>> Insert size mean insert size = 81,993.6637 std insert size = 2,751,737.7239 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.666 >>>>>>> ACTG content number of A's = 4,210,591,786 bp (29.63%) number of C's = 2,874,313,092 bp (20.23%) number of T's = 4,232,460,548 bp (29.78%) number of G's = 2,882,804,807 bp (20.29%) number of N's = 11,300,827 bp (0.08%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 67,337,132 number of insertions = 1,411,812 mapped reads with insertion percentage = 0.94% number of deletions = 2,917,998 mapped reads with deletion percentage = 1.94% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 4.5922X std coverageData = 289.9814X There is a 28.18% of reference with a coverageData >= 1X There is a 21.66% of reference with a coverageData >= 2X There is a 16.9% of reference with a coverageData >= 3X There is a 14.27% of reference with a coverageData >= 4X There is a 12.25% of reference with a coverageData >= 5X There is a 10.78% of reference with a coverageData >= 6X There is a 9.61% of reference with a coverageData >= 7X There is a 8.67% of reference with a coverageData >= 8X There is a 7.89% of reference with a coverageData >= 9X There is a 7.24% of reference with a coverageData >= 10X There is a 6.68% of reference with a coverageData >= 11X There is a 6.19% of reference with a coverageData >= 12X There is a 5.77% of reference with a coverageData >= 13X There is a 5.4% of reference with a coverageData >= 14X There is a 5.07% of reference with a coverageData >= 15X There is a 4.77% of reference with a coverageData >= 16X There is a 4.51% of reference with a coverageData >= 17X There is a 4.26% of reference with a coverageData >= 18X There is a 4.05% of reference with a coverageData >= 19X There is a 3.85% of reference with a coverageData >= 20X There is a 3.66% of reference with a coverageData >= 21X There is a 3.5% of reference with a coverageData >= 22X There is a 3.34% of reference with a coverageData >= 23X There is a 3.2% of reference with a coverageData >= 24X There is a 3.07% of reference with a coverageData >= 25X There is a 2.94% of reference with a coverageData >= 26X There is a 2.83% of reference with a coverageData >= 27X There is a 2.72% of reference with a coverageData >= 28X There is a 2.62% of reference with a coverageData >= 29X There is a 2.53% of reference with a coverageData >= 30X There is a 2.44% of reference with a coverageData >= 31X There is a 2.36% of reference with a coverageData >= 32X There is a 2.28% of reference with a coverageData >= 33X There is a 2.2% of reference with a coverageData >= 34X There is a 2.13% of reference with a coverageData >= 35X There is a 2.07% of reference with a coverageData >= 36X There is a 2% of reference with a coverageData >= 37X There is a 1.94% of reference with a coverageData >= 38X There is a 1.89% of reference with a coverageData >= 39X There is a 1.83% of reference with a coverageData >= 40X There is a 1.78% of reference with a coverageData >= 41X There is a 1.73% of reference with a coverageData >= 42X There is a 1.69% of reference with a coverageData >= 43X There is a 1.64% of reference with a coverageData >= 44X There is a 1.6% of reference with a coverageData >= 45X There is a 1.56% of reference with a coverageData >= 46X There is a 1.52% of reference with a coverageData >= 47X There is a 1.48% of reference with a coverageData >= 48X There is a 1.45% of reference with a coverageData >= 49X There is a 1.41% of reference with a coverageData >= 50X There is a 1.38% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 954040769 3.827636477583741 30.863508932996538 chr2 243199373 1039816123 4.275570739238707 32.18588617762918 chr3 198022430 781696614 3.9475155112478926 23.761019696117955 chr4 191154276 875509017 4.580117355052 32.925037575025144 chr5 180915260 878526306 4.856009968423891 40.72340741878107 chr6 171115067 2703132130 15.797160223184788 1217.5765556341914 chr7 159138663 614196831 3.859507296476407 29.015048726612115 chr8 146364022 645388064 4.409472049080477 30.226724584163456 chr9 141213431 474929293 3.3632019959914436 22.809959831095743 chr10 135534747 499078585 3.682292519423082 21.74266652381257 chr11 135006516 618950108 4.584594331728403 51.420214904218625 chr12 133851895 536813936 4.010506806795675 28.336163840522964 chr13 115169878 632460106 5.491540991299826 186.02098386015535 chr14 107349540 334613866 3.1170498355186247 18.20424030162158 chr15 102531392 294917500 2.876362977691749 18.50829724976765 chr16 90354753 250407887 2.7713858838173127 34.21513929279399 chr17 81195210 233499387 2.8757778568464816 20.72317913388387 chr18 78077248 321736467 4.120745482730129 34.59182105004913 chr19 59128983 129034773 2.182259299132542 22.09190474539117 chr20 63025520 200327291 3.178510720736616 20.096029708918472 chr21 48129895 117585425 2.4430850098467904 14.983635049708669 chr22 51304566 68828599 1.3415686822104684 10.85463889746609 chrMT 16571 14355 0.8662724035966447 4.617099723316961 chrX 155270560 999321494 6.436001093832598 41.80387647607544 chrY 59373566 11203296 0.1886916477275426 3.406304743863244