BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 3,626,734 number of mapped reads = 3,058,584 (84.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,555,356 number of mapped paired reads (second in pair) = 1,503,228 number of mapped paired reads (both in pair) = 2,812,202 number of mapped paired reads (singletons) = 246,382 number of mapped bases = 117,992,655 bp number of sequenced bases = 117,979,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,227 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 63,210.6955 std insert size = 2,428,110.0704 median insert size = 90 >>>>>>> Mapping quality mean mapping quality = 45.8006 >>>>>>> ACTG content number of A's = 30,269,634 bp (25.66%) number of C's = 27,396,701 bp (23.22%) number of T's = 31,369,272 bp (26.59%) number of G's = 28,938,492 bp (24.53%) number of N's = 5,803 bp (0%) GC percentage = 47.75% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 552,566 number of insertions = 4,151 mapped reads with insertion percentage = 0.14% number of deletions = 9,898 mapped reads with deletion percentage = 0.32% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.2741X There is a 2.72% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 10136835 0.040669246717744384 0.2812982838360696 chr2 243199373 10034490 0.0412603448611687 0.30538947292482155 chr3 198022430 7758940 0.03918212699440159 0.2614504486529975 chr4 191154276 6768845 0.03541037711340551 0.25582023821361294 chr5 180915260 6853099 0.03788016002630182 0.2580089677988795 chr6 171115067 6453368 0.0377136164169576 0.26985915712368075 chr7 159138663 6343980 0.03986447969592405 0.28786504495448484 chr8 146364022 5775552 0.039460189198681626 0.2785110788321045 chr9 141213431 5093802 0.03607165383581679 0.2589339852763259 chr10 135534747 5835928 0.04305853760143146 0.2832891014375122 chr11 135006516 5546085 0.04108012831025134 0.34070325399127566 chr12 133851895 5709910 0.042658417350012114 0.2767545465092123 chr13 115169878 3846707 0.03340028718273019 0.24790352534014098 chr14 107349540 3565998 0.03321856805348211 0.24617701044258922 chr15 102531392 3677621 0.035868244137366244 0.25537663160826335 chr16 90354753 3958006 0.04380517757599315 0.3010026085817153 chr17 81195210 3897096 0.047996624431416585 0.302301003114633 chr18 78077248 3194348 0.040912661265929864 0.28272819685078177 chr19 59128983 2992203 0.05060467554464788 0.3349634870035374 chr20 63025520 2913133 0.04622148298022769 0.2912713425419771 chr21 48129895 1559222 0.032396123033303935 0.2550072598741076 chr22 51304566 1898720 0.0370087917710872 0.2811671870239765 chrMT 16571 16131 0.9734475891617886 1.7855126063119426 chrX 155270560 3417797 0.022011880423436356 0.19486147782301838 chrY 59373566 744839 0.012544959822692813 0.15795518136212808