BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617655.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,599,207 (92.5%) number of supplementary alignments = 169,915 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,989,383 number of mapped paired reads (second in pair) = 14,609,824 number of mapped paired reads (both in pair) = 28,783,088 number of mapped paired reads (singletons) = 816,119 number of mapped bases = 2,851,281,025 bp number of sequenced bases = 2,849,567,078 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,659,310 duplication rate = 10.54% >>>>>>> Insert size mean insert size = 47,575.3673 std insert size = 2,051,282.4435 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.4574 >>>>>>> ACTG content number of A's = 849,523,247 bp (29.81%) number of C's = 565,575,380 bp (19.85%) number of T's = 847,230,443 bp (29.73%) number of G's = 582,979,598 bp (20.46%) number of N's = 4,258,410 bp (0.15%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0166 number of mismatches = 46,471,543 number of insertions = 445,655 mapped reads with insertion percentage = 1.48% number of deletions = 1,038,346 mapped reads with deletion percentage = 3.44% homopolymer indels = 47.53% >>>>>>> Coverage mean coverageData = 0.921X std coverageData = 10.1778X There is a 32.87% of reference with a coverageData >= 1X There is a 18.85% of reference with a coverageData >= 2X There is a 11.41% of reference with a coverageData >= 3X There is a 7.23% of reference with a coverageData >= 4X There is a 4.72% of reference with a coverageData >= 5X There is a 3.18% of reference with a coverageData >= 6X There is a 2.19% of reference with a coverageData >= 7X There is a 1.55% of reference with a coverageData >= 8X There is a 1.11% of reference with a coverageData >= 9X There is a 0.82% of reference with a coverageData >= 10X There is a 0.62% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175002653 0.7021152135865691 9.955085654811903 chr2 243199373 294771571 1.2120572819075484 11.744606986442545 chr3 198022430 239173865 1.207811988773191 2.4337397239563376 chr4 191154276 159329926 0.833514841174675 7.825366588322229 chr5 180915260 188698979 1.0430241152681095 2.291346884368963 chr6 171115067 138261761 0.8080045984495334 5.7144747289144115 chr7 159138663 223278711 1.403045035008243 12.986723833319425 chr8 146364022 126791114 0.8662724094859869 3.9594247567854133 chr9 141213431 116909021 0.8278888217084677 19.210974739565927 chr10 135534747 120632952 0.8900518477376137 20.762894897197917 chr11 135006516 156943140 1.162485668469513 11.62815543280619 chr12 133851895 121734134 0.909468887235403 2.195200449758919 chr13 115169878 122777898 1.066059113130258 2.282088932679775 chr14 107349540 81393600 0.7582109806898101 2.4148622164619225 chr15 102531392 61025650 0.5951899102276891 1.7497859362637431 chr16 90354753 79193999 0.8764785068916076 16.327705561640506 chr17 81195210 69938499 0.8613623759332601 12.180451949372879 chr18 78077248 52400931 0.6711421360547953 17.48258047685969 chr19 59128983 30204227 0.5108193218882185 5.808379383148082 chr20 63025520 76745712 1.2176926425993788 2.949068895093297 chr21 48129895 41527888 0.8628293911715369 4.118702636987808 chr22 51304566 18163819 0.3540390342645136 1.2451055209967659 chrMT 16571 3024644 182.52634119847926 128.02001062768042 chrX 155270560 141969867 0.9143386035317964 4.2434472079339285 chrY 59373566 11386464 0.191776656972229 16.2366155212416