BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819068.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 811,640 number of mapped reads = 734,320 (90.47%) number of supplementary alignments = 2,801 (0.35%) number of secondary alignments = 0 number of mapped bases = 42,248,311 bp number of sequenced bases = 42,236,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,527 duplication rate = 1.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5908 >>>>>>> ACTG content number of A's = 10,779,606 bp (25.52%) number of C's = 8,180,031 bp (19.37%) number of T's = 13,231,686 bp (31.33%) number of G's = 10,044,760 bp (23.78%) number of N's = 872 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 201,459 number of insertions = 2,953 mapped reads with insertion percentage = 0.4% number of deletions = 6,693 mapped reads with deletion percentage = 0.9% homopolymer indels = 39.17% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.1372X There is a 1.28% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4736645 0.019003543425474556 0.1867605963182327 chr2 243199373 3532503 0.01452513201997441 0.15051239725583485 chr3 198022430 2760097 0.013938304867786947 0.12315846874289985 chr4 191154276 2689053 0.014067448849535544 0.1294696411685585 chr5 180915260 2131110 0.011779603334732516 0.11395868427761444 chr6 171115067 2215855 0.012949502570688295 0.12275180581504865 chr7 159138663 1807692 0.011359225758984792 0.12171753977094726 chr8 146364022 2713218 0.018537465443522725 0.15224822477101196 chr9 141213431 1531445 0.01084489619121286 0.13357292950426114 chr10 135534747 1998233 0.014743326299933994 0.14451831540178803 chr11 135006516 1313224 0.00972711568973456 0.11804266073746078 chr12 133851895 1914477 0.014302950286957088 0.1260157389904191 chr13 115169878 1305034 0.011331383020133094 0.11099031600228428 chr14 107349540 1496813 0.013943357372560703 0.12694572381445873 chr15 102531392 1221119 0.011909708589541046 0.11396612204032466 chr16 90354753 1238872 0.013711199011301597 0.12689817182960947 chr17 81195210 925814 0.011402322871016652 0.11324325024220268 chr18 78077248 1032752 0.013227310470778889 0.22052161602203077 chr19 59128983 794408 0.013435171039556016 0.14339074469763075 chr20 63025520 1354514 0.0214915164523831 0.15573574583437344 chr21 48129895 553195 0.011493791956122074 0.11829887370370365 chr22 51304566 494393 0.009636432749474969 0.10236279276125457 chrMT 16571 3932 0.23728199867237945 0.5285299089515556 chrX 155270560 2367403 0.015246953446938041 0.13607024163479214 chrY 59373566 116510 0.0019623210773629463 0.05579197431639693