BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006363.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 = 4,977,774 number of mapped reads = 3,937,156 (79.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,989,747 number of mapped paired reads (second in pair) = 1,947,409 number of mapped paired reads (both in pair) = 3,574,362 number of mapped paired reads (singletons) = 362,794 number of mapped bases = 152,167,019 bp number of sequenced bases = 152,142,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 310,710 duplication rate = 7.45% >>>>>>> Insert size mean insert size = 77,448.5695 std insert size = 2,613,397.2288 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 47.9673 >>>>>>> ACTG content number of A's = 42,642,441 bp (28.03%) number of C's = 32,579,465 bp (21.41%) number of T's = 43,498,714 bp (28.59%) number of G's = 33,415,920 bp (21.96%) number of N's = 6,303 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 621,103 number of insertions = 4,350 mapped reads with insertion percentage = 0.11% number of deletions = 17,460 mapped reads with deletion percentage = 0.44% homopolymer indels = 41.55% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.3671X There is a 4% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 12844861 0.05153391774297726 0.5108173027784891 chr2 243199373 12883083 0.05297333969689141 0.31191319383899485 chr3 198022430 10725703 0.05416408131139488 0.27431439846417194 chr4 191154276 8318954 0.043519581011099116 0.24944790899121688 chr5 180915260 9621435 0.05318199802493167 0.2870151511825655 chr6 171115067 8695474 0.05081653037601885 0.27782338482743335 chr7 159138663 8333854 0.052368505823126084 0.3747194940055486 chr8 146364022 7656384 0.05231056030969141 0.904917921624177 chr9 141213431 6704856 0.04748029951910169 0.27959426990147035 chr10 135534747 6817385 0.050299905750368204 0.31201660401755055 chr11 135006516 7239034 0.0536198860209088 0.30347928056537654 chr12 133851895 6938203 0.051834925459964536 0.2709320327735215 chr13 115169878 4483312 0.038927817567020434 0.23449632478032398 chr14 107349540 4753927 0.04428455864831838 0.3293029949485324 chr15 102531392 4490546 0.04379679152312689 0.2481057268174403 chr16 90354753 4655093 0.051520178468087895 0.3013544052337033 chr17 81195210 4140275 0.05099161637737004 0.27634115231711914 chr18 78077248 3850481 0.04931630018517046 0.3987558872949778 chr19 59128983 2974985 0.050313481630489064 0.3746537180579257 chr20 63025520 3321172 0.052695669944492325 0.2774869845882113 chr21 48129895 1983156 0.04120424530325695 0.24873780241490687 chr22 51304566 1968828 0.03837529782436908 0.23550191559953512 chrMT 16571 16166 0.9755597127511918 1.3180737111817367 chrX 155270560 8412191 0.054177630324769875 0.29057973792166136 chrY 59373566 337661 0.005687059456728606 0.15688240295770103