BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124863.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,537,948 number of mapped reads = 4,380,829 (96.54%) number of supplementary alignments = 14,530 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,194,288 number of mapped paired reads (second in pair) = 2,186,541 number of mapped paired reads (both in pair) = 4,365,190 number of mapped paired reads (singletons) = 15,639 number of mapped bases = 380,769,467 bp number of sequenced bases = 380,552,541 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 397,759 duplication rate = 6.82% >>>>>>> Insert size mean insert size = 36,182.7275 std insert size = 1,808,618.9052 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.8037 >>>>>>> ACTG content number of A's = 106,477,306 bp (27.98%) number of C's = 71,780,186 bp (18.86%) number of T's = 112,235,676 bp (29.49%) number of G's = 89,915,926 bp (23.63%) number of N's = 143,447 bp (0.04%) GC percentage = 42.49% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 2,903,977 number of insertions = 53,539 mapped reads with insertion percentage = 1.19% number of deletions = 128,550 mapped reads with deletion percentage = 2.87% homopolymer indels = 47.92% >>>>>>> Coverage mean coverageData = 0.123X std coverageData = 0.9992X There is a 8.26% of reference with a coverageData >= 1X There is a 2.42% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 28592932 0.11471558981592267 1.0170540852991605 chr2 243199373 34773759 0.1429845750465812 1.3403197864091307 chr3 198022430 30361607 0.15332408050946553 0.5388065295500668 chr4 191154276 22336580 0.11685106118159763 0.7319296827615166 chr5 180915260 24388130 0.13480416190430813 0.520655392869719 chr6 171115067 20081439 0.1173563459493605 0.7874531072888891 chr7 159138663 26719283 0.16789938093170986 1.4811830591830653 chr8 146364022 19149047 0.13083165342368086 0.5687914238784708 chr9 141213431 12910142 0.09142290438364889 1.037212553802004 chr10 135534747 17855952 0.1317444595960326 2.4198948618739258 chr11 135006516 20662381 0.1530472869916886 0.8041935471301823 chr12 133851895 18464510 0.13794731856429826 0.5090578006264973 chr13 115169878 11001239 0.09552184295966694 0.41921289151068686 chr14 107349540 7545556 0.07028959788742457 0.40232162236350894 chr15 102531392 12902195 0.12583653404412962 0.508170401414864 chr16 90354753 10649741 0.1178658636806854 1.0398739665422583 chr17 81195210 10209861 0.12574462212733978 1.3443989864986015 chr18 78077248 9169673 0.11744359893422474 1.2151738776339802 chr19 59128983 4047616 0.06845401010871437 0.6962487991957556 chr20 63025520 9482764 0.15045911560904218 0.5824567318653455 chr21 48129895 5378818 0.11175627954309894 0.5423299345854116 chr22 51304566 3398308 0.06623792510007784 0.3895111584089447 chrMT 16571 84397 5.093054130710277 4.1130294315710865 chrX 155270560 19736616 0.12711112782745165 0.6258481059259052 chrY 59373566 866921 0.014601127377122674 0.9781805868227385