BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617485.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 = 30,545,177 (95.45%) number of supplementary alignments = 136,887 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,433,292 number of mapped paired reads (second in pair) = 15,111,885 number of mapped paired reads (both in pair) = 29,965,504 number of mapped paired reads (singletons) = 579,673 number of mapped bases = 2,982,100,744 bp number of sequenced bases = 2,980,324,254 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,314,744 duplication rate = 10.01% >>>>>>> Insert size mean insert size = 29,645.6629 std insert size = 1,591,251.5515 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.7808 >>>>>>> ACTG content number of A's = 877,990,907 bp (29.46%) number of C's = 603,067,041 bp (20.23%) number of T's = 877,869,763 bp (29.46%) number of G's = 618,390,897 bp (20.75%) number of N's = 3,005,646 bp (0.1%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 34,240,743 number of insertions = 442,503 mapped reads with insertion percentage = 1.42% number of deletions = 1,039,797 mapped reads with deletion percentage = 3.33% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.9633X std coverageData = 9.6857X There is a 38.33% of reference with a coverageData >= 1X There is a 20.69% of reference with a coverageData >= 2X There is a 11.7% of reference with a coverageData >= 3X There is a 6.96% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 2.76% of reference with a coverageData >= 6X There is a 1.82% of reference with a coverageData >= 7X There is a 1.25% of reference with a coverageData >= 8X There is a 0.88% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% 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 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191909313 0.7699451749811287 9.357756243067271 chr2 243199373 307988708 1.2664042024483344 11.510334457886918 chr3 198022430 246498244 1.2447996118419515 2.2212492262653725 chr4 191154276 154161709 0.8064779518717122 6.168533570028778 chr5 180915260 190878346 1.0550704567431184 2.0781460997376735 chr6 171115067 140305403 0.8199476846770016 5.353509889317861 chr7 159138663 229695401 1.4433664118442417 13.043740966988905 chr8 146364022 132479937 0.9051400418608339 3.8237694110510123 chr9 141213431 123677431 0.8758191775681734 18.60585661777848 chr10 135534747 126613745 0.9341792256416726 18.536832412292664 chr11 135006516 168301166 1.2466151337465816 12.644846854242044 chr12 133851895 130047930 0.9715807908434916 1.9671429918496486 chr13 115169878 126502085 1.0983955804832928 2.1195885530616287 chr14 107349540 86798034 0.8085552485832729 2.1972957015486894 chr15 102531392 67531223 0.6586394828229778 1.4521083816817146 chr16 90354753 80297795 0.888694754109947 14.712187059545444 chr17 81195210 83529422 1.028748149059532 13.420574932599912 chr18 78077248 53394408 0.6838664190623112 17.033449737783766 chr19 59128983 35632091 0.6026163345309017 5.83568291184967 chr20 63025520 88339718 1.4016499665532312 2.801012693159841 chr21 48129895 42889095 0.8911113352730148 3.822519637098322 chr22 51304566 22366013 0.43594585713871936 1.2542497495108302 chrMT 16571 2086023 125.88395389535937 92.53183668109553 chrX 155270560 139930725 0.9012057726847897 4.078889751704216 chrY 59373566 10246779 0.1725814986420051 13.669656430321416