BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006013.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 = 12,548,910 number of mapped reads = 8,045,349 (64.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,040,935 number of mapped paired reads (second in pair) = 4,004,414 number of mapped paired reads (both in pair) = 7,233,006 number of mapped paired reads (singletons) = 812,343 number of mapped bases = 309,797,725 bp number of sequenced bases = 309,752,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 378,595 duplication rate = 4.04% >>>>>>> Insert size mean insert size = 73,675.8134 std insert size = 2,634,928.4407 median insert size = 69 >>>>>>> Mapping quality mean mapping quality = 44.7577 >>>>>>> ACTG content number of A's = 84,534,763 bp (27.29%) number of C's = 68,612,080 bp (22.15%) number of T's = 86,545,490 bp (27.94%) number of G's = 69,991,273 bp (22.6%) number of N's = 69,183 bp (0.02%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,643,439 number of insertions = 11,014 mapped reads with insertion percentage = 0.14% number of deletions = 33,219 mapped reads with deletion percentage = 0.41% homopolymer indels = 41.33% >>>>>>> Coverage mean coverageData = 0.1001X std coverageData = 0.7309X There is a 6.6% of reference with a coverageData >= 1X There is a 2.25% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 25518754 0.10238190740555868 0.7710121838769516 chr2 243199373 26559027 0.10920680704222045 0.6152799689050011 chr3 198022430 21290033 0.10751323978803816 0.45598025113206303 chr4 191154276 20048447 0.1048809758249928 0.47010646538694467 chr5 180915260 18594344 0.10277930120433179 0.4421989288591732 chr6 171115067 17719610 0.10355376829557622 0.5151721273971787 chr7 159138663 17186239 0.10799537130709713 0.6236946666732421 chr8 146364022 15635801 0.10682817256825589 1.2789446235365458 chr9 141213431 12663819 0.08967857313798996 0.4555180288460674 chr10 135534747 14383305 0.10612263879461109 0.5449812112287961 chr11 135006516 14053873 0.10409773851211744 0.4880979149722732 chr12 133851895 14232396 0.1063294322430026 0.4690505933909635 chr13 115169878 9918134 0.08611743080946913 0.41418161469638787 chr14 107349540 9529412 0.08876993790564916 0.4380303606292609 chr15 102531392 8938469 0.08717787621570572 0.41895352564416355 chr16 90354753 8875514 0.09822963048772874 0.501178174807212 chr17 81195210 8707345 0.10723963889002812 0.46972508069066504 chr18 78077248 7877285 0.10089091511012273 0.585614001747148 chr19 59128983 7044172 0.11913230437262891 3.234442155128252 chr20 63025520 6435375 0.10210744790364285 0.45927144675774784 chr21 48129895 4120415 0.0856103051959702 0.4345285658516492 chr22 51304566 3908623 0.07618470059760372 0.4875984867015258 chrMT 16571 136548 8.240178625309275 5.832940961799272 chrX 155270560 15586794 0.10038473487826668 0.45385547464344533 chrY 59373566 833991 0.014046503455763462 0.25376827602323426