BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617675.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 = 28,533,748 number of mapped reads = 26,160,759 (91.68%) number of supplementary alignments = 166,799 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,300,274 number of mapped paired reads (second in pair) = 12,860,485 number of mapped paired reads (both in pair) = 25,328,940 number of mapped paired reads (singletons) = 831,819 number of mapped bases = 2,515,730,959 bp number of sequenced bases = 2,514,225,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,621,901 duplication rate = 10.21% >>>>>>> Insert size mean insert size = 51,864.7488 std insert size = 2,135,248.6724 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 52.3596 >>>>>>> ACTG content number of A's = 751,610,337 bp (29.89%) number of C's = 498,205,784 bp (19.82%) number of T's = 749,000,542 bp (29.79%) number of G's = 512,811,531 bp (20.4%) number of N's = 2,596,815 bp (0.1%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0162 number of mismatches = 39,928,998 number of insertions = 393,916 mapped reads with insertion percentage = 1.48% number of deletions = 912,443 mapped reads with deletion percentage = 3.41% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.8127X std coverageData = 9.0836X There is a 31.01% of reference with a coverageData >= 1X There is a 17.03% of reference with a coverageData >= 2X There is a 9.9% of reference with a coverageData >= 3X There is a 6.06% of reference with a coverageData >= 4X There is a 3.83% of reference with a coverageData >= 5X There is a 2.51% of reference with a coverageData >= 6X There is a 1.68% of reference with a coverageData >= 7X There is a 1.16% of reference with a coverageData >= 8X There is a 0.82% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% 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 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% 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 0.03% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 154212501 0.6187045808804624 8.800589259411106 chr2 243199373 259980049 1.068999668021348 10.389221698223615 chr3 198022430 210720791 1.0641258720034896 2.211414560053052 chr4 191154276 140938066 0.7373000957613943 7.00698597865644 chr5 180915260 166357077 0.9195303757129166 2.0538864213149624 chr6 171115067 122048350 0.7132530883443479 4.976526473456381 chr7 159138663 196739600 1.2362778239502992 11.50951197493965 chr8 146364022 111971420 0.7650201085619251 3.522745135267181 chr9 141213431 103325505 0.7316974332278634 17.425385709086157 chr10 135534747 106393710 0.7849921319438475 18.49385031686048 chr11 135006516 138434682 1.025392596606226 10.285876391091636 chr12 133851895 107693072 0.8045689005747734 2.1491098799075488 chr13 115169878 108231930 0.9397590053885444 2.1204570171002155 chr14 107349540 71993009 0.6706410572416053 2.174668642371069 chr15 102531392 53757410 0.524301962076161 1.7901720051151628 chr16 90354753 69902010 0.773639545005452 14.61125022041588 chr17 81195210 61605426 0.7587322700440088 10.837209060184119 chr18 78077248 46416747 0.5944977338340613 15.516262735446428 chr19 59128983 26409235 0.44663773432396087 5.206031949246258 chr20 63025520 67494803 1.070912274900707 2.6546292476469877 chr21 48129895 36737498 0.7632989434113663 3.69621514536738 chr22 51304566 15982112 0.31151441764462057 1.1455788900144543 chrMT 16571 2630169 158.7211996861988 111.10215955565161 chrX 155270560 125631060 0.8091106259937493 3.86685389658167 chrY 59373566 10124727 0.17052583636293633 14.600514974562953