BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006210.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 2,685,594 number of mapped reads = 2,200,787 (81.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,103,647 number of mapped paired reads (second in pair) = 1,097,140 number of mapped paired reads (both in pair) = 2,030,980 number of mapped paired reads (singletons) = 169,807 number of mapped bases = 85,194,828 bp number of sequenced bases = 85,183,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,894 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 53,661.5759 std insert size = 2,195,751.0626 median insert size = 119 >>>>>>> Mapping quality mean mapping quality = 48.0489 >>>>>>> ACTG content number of A's = 23,605,187 bp (27.71%) number of C's = 18,365,585 bp (21.56%) number of T's = 24,118,108 bp (28.31%) number of G's = 19,090,836 bp (22.41%) number of N's = 4,085 bp (0%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 248,372 number of insertions = 2,640 mapped reads with insertion percentage = 0.12% number of deletions = 8,446 mapped reads with deletion percentage = 0.38% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2102X There is a 2.41% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 7083930 0.02842091213887086 0.2575345880909779 chr2 243199373 7223739 0.029702950755551495 0.2168004029070784 chr3 198022430 5595508 0.02825694038801564 0.1864674832390128 chr4 191154276 5326161 0.02786315384333856 0.19267329417131776 chr5 180915260 5066810 0.028006537425311718 0.18561016417177342 chr6 171115067 4899402 0.028632206888011796 0.19846929394314197 chr7 159138663 4516221 0.028379156358753623 0.23389429503649958 chr8 146364022 4199317 0.028690910119974704 0.27205588214656706 chr9 141213431 3474467 0.02460436642177471 0.18984316599622655 chr10 135534747 4117071 0.030376498212668666 0.22678453165991186 chr11 135006516 3987270 0.029533907830048736 0.21054374181576552 chr12 133851895 3770486 0.02816908942529353 0.1869289213059618 chr13 115169878 2680258 0.02327221359043204 0.1688046952221379 chr14 107349540 2602604 0.024244202630025243 0.22929337214124237 chr15 102531392 2460538 0.02399789910196479 0.17239862320436353 chr16 90354753 2556769 0.028297006135360694 0.19968917992624666 chr17 81195210 2454710 0.03023220212128277 0.19903200922167358 chr18 78077248 2263424 0.028989546352863257 0.2614179604483622 chr19 59128983 1831837 0.030980356959631795 0.22572215826470907 chr20 63025520 1925198 0.030546324726872544 0.19535939066632627 chr21 48129895 1112087 0.023105951093390087 0.18016203637554262 chr22 51304566 1113347 0.021700739072619775 0.17064965150686684 chrMT 16571 848 0.05117373725182548 0.2680460627190972 chrX 155270560 4729687 0.030460938635115377 0.2019930404609307 chrY 59373566 203139 0.003421371052565716 0.09622398854830361