BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089573.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 26,200,240 number of mapped reads = 21,676,277 (82.73%) number of supplementary alignments = 839 (0%) number of secondary alignments = 0 number of mapped bases = 1,013,759,878 bp number of sequenced bases = 1,013,545,057 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,526,169 duplication rate = 8.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8172 >>>>>>> ACTG content number of A's = 323,205,614 bp (31.89%) number of C's = 202,687,979 bp (20%) number of T's = 269,496,927 bp (26.59%) number of G's = 218,123,639 bp (21.52%) number of N's = 30,898 bp (0%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 5,147,505 number of insertions = 45,321 mapped reads with insertion percentage = 0.21% number of deletions = 142,826 mapped reads with deletion percentage = 0.66% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.3275X std coverageData = 1.681X There is a 16.47% of reference with a coverageData >= 1X There is a 6.94% of reference with a coverageData >= 2X There is a 3.45% of reference with a coverageData >= 3X There is a 1.9% of reference with a coverageData >= 4X There is a 1.13% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% 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 0.02% 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% 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 79374808 0.3184538023678585 2.2501411403647356 chr2 243199373 84984513 0.34944379975848044 1.9806291198324488 chr3 198022430 68138439 0.3440945502991757 1.0802568310323797 chr4 191154276 66863933 0.3497904122218014 1.1904128980173814 chr5 180915260 61933932 0.34233669398590255 1.0974642938835342 chr6 171115067 65564452 0.383160017112929 1.4022324630437284 chr7 159138663 54756299 0.34407916949760975 2.2705622864052937 chr8 146364022 50954102 0.34813269889508774 3.305987839902716 chr9 141213431 41910572 0.2967888514797151 1.5167722476889474 chr10 135534747 46511025 0.3431667969247768 1.5500433513666745 chr11 135006516 45562985 0.3374873032054245 1.5507385503553353 chr12 133851895 45602935 0.34069696958716944 1.14179804381114 chr13 115169878 32620233 0.28323580407022747 0.9800911778949231 chr14 107349540 29505413 0.27485365097978065 1.2296563327734815 chr15 102531392 27822822 0.27135905850180986 0.9554131629646178 chr16 90354753 27904255 0.308829962713749 1.1600220299466966 chr17 81195210 27637469 0.34038299796256455 1.2841978618917078 chr18 78077248 29978447 0.3839588070522158 2.3739516170272563 chr19 59128983 18432315 0.31173062793926287 2.1051191860497966 chr20 63025520 20683662 0.3281791566336938 1.164304965412848 chr21 48129895 13048922 0.27111885450820117 1.1853803821603195 chr22 51304566 10924802 0.21294015039519096 0.8570094097178803 chrMT 16571 526519 31.77352000482771 27.19066193109666 chrX 155270560 59719414 0.38461517753268876 1.4500069879576405 chrY 59373566 2797610 0.047118780098200606 0.6812674610124639