BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081166.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 = 2,074,223 number of mapped reads = 1,878,946 (90.59%) number of supplementary alignments = 18,914 (0.91%) number of secondary alignments = 0 number of mapped bases = 127,688,944 bp number of sequenced bases = 127,641,797 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,397 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4561 >>>>>>> ACTG content number of A's = 36,756,715 bp (28.8%) number of C's = 23,608,581 bp (18.5%) number of T's = 40,169,146 bp (31.47%) number of G's = 27,068,875 bp (21.21%) number of N's = 38,480 bp (0.03%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,046,606 number of insertions = 9,951 mapped reads with insertion percentage = 0.52% number of deletions = 29,022 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.3444X There is a 3.55% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10087221 0.04047019405420057 0.6497029278228789 chr2 243199373 11108611 0.04567697220173343 0.3303362821071087 chr3 198022430 9571985 0.0483378827337893 0.24714033906799213 chr4 191154276 8206407 0.042930805272700254 0.24040692045736398 chr5 180915260 9143151 0.05053830727159224 0.25367209051782125 chr6 171115067 7800274 0.04558496301205317 0.26889823226381177 chr7 159138663 6147219 0.03862806739805273 0.31855719754399037 chr8 146364022 6847389 0.04678327984181796 0.5342454616732153 chr9 141213431 4677350 0.03312255758448359 0.2960981613613592 chr10 135534747 5804075 0.04282352037739813 0.29305542930465733 chr11 135006516 6011147 0.04452486574796138 0.29783031608621585 chr12 133851895 5703365 0.042609520022111005 0.235801113095593 chr13 115169878 4257883 0.03697045680642294 0.21605946323334946 chr14 107349540 3768150 0.035101687440859085 0.2273081612885789 chr15 102531392 3566241 0.034781942685416775 0.21129339119532384 chr16 90354753 3170199 0.03508613431769328 0.23490555367032723 chr17 81195210 2819316 0.03472268869062596 0.24043415692078274 chr18 78077248 2764414 0.035406140339372616 0.6038096571622519 chr19 59128983 2096957 0.035464114104583874 0.45008463142191685 chr20 63025520 2260060 0.03585944233383556 0.22129262764701296 chr21 48129895 1800878 0.03741703571138063 0.23037418166128626 chr22 51304566 1086756 0.021182442124157135 0.16114132894908323 chrMT 16571 10868 0.65584454770382 0.8924825181086238 chrX 155270560 8682508 0.05591857207187248 0.2947074818869089 chrY 59373566 296520 0.004994141669038373 0.10736177129205564