BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080757.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,342,984 number of mapped reads = 4,564,757 (71.97%) number of supplementary alignments = 42,258 (0.67%) number of secondary alignments = 0 number of mapped bases = 287,747,549 bp number of sequenced bases = 287,646,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 298,402 duplication rate = 5.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.131 >>>>>>> ACTG content number of A's = 88,952,614 bp (30.92%) number of C's = 57,739,100 bp (20.07%) number of T's = 73,933,213 bp (25.7%) number of G's = 66,922,556 bp (23.27%) number of N's = 98,530 bp (0.03%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 2,410,657 number of insertions = 23,617 mapped reads with insertion percentage = 0.51% number of deletions = 54,050 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.08% >>>>>>> Coverage mean coverageData = 0.093X std coverageData = 0.6113X There is a 6.73% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 39235902 0.1574154633700993 0.8632841454159786 chr2 243199373 21890025 0.09000855853357813 0.6433137138062812 chr3 198022430 15614186 0.0788505928343572 0.3661750839397487 chr4 191154276 15803718 0.08267520000441947 0.5538178504027425 chr5 180915260 21203524 0.11720141241816749 0.4557811028626065 chr6 171115067 18760456 0.10963649390383606 0.7416714454707819 chr7 159138663 19460954 0.12228928930991459 0.9053750541989517 chr8 146364022 11302596 0.07722250212555651 0.5485388645226886 chr9 141213431 9831114 0.06961883108696651 0.43287882660211097 chr10 135534747 13204680 0.0974265293017443 1.0915193372610588 chr11 135006516 9311270 0.06896904146463567 0.43666076763801803 chr12 133851895 12491879 0.09332612735889918 0.41169135805741963 chr13 115169878 10447718 0.09071571648274213 0.3999680747089283 chr14 107349540 8407625 0.0783200840916505 0.42892515575421636 chr15 102531392 7555072 0.07368545235394834 0.3541595132428502 chr16 90354753 6350285 0.07028169287342305 0.459450635518435 chr17 81195210 8461412 0.10421072868707403 0.48894818685253644 chr18 78077248 4130608 0.052904118751726494 0.7074880707269767 chr19 59128983 6393222 0.1081233208425046 0.7343798886214358 chr20 63025520 5972131 0.09475734591321103 0.43390128374629594 chr21 48129895 4326403 0.0898901400054997 0.5518791911913452 chr22 51304566 2030328 0.03957402154030501 0.2561545150173149 chrMT 16571 30274 1.826926558445477 2.0311898745067074 chrX 155270560 14522329 0.0935291854424947 0.4369013696240591 chrY 59373566 1009838 0.017008208669831285 0.5846590274270311