BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046453.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 5,366,800 number of mapped reads = 5,240,517 (97.65%) number of supplementary alignments = 35,627 (0.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,673,154 number of mapped paired reads (second in pair) = 2,567,363 number of mapped paired reads (both in pair) = 5,124,696 number of mapped paired reads (singletons) = 115,821 number of mapped bases = 504,658,663 bp number of sequenced bases = 504,507,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,406,638 duplication rate = 31% >>>>>>> Insert size mean insert size = 58,759.1725 std insert size = 2,275,691.9049 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 51.2791 >>>>>>> ACTG content number of A's = 149,620,316 bp (29.66%) number of C's = 103,003,351 bp (20.42%) number of T's = 149,338,602 bp (29.6%) number of G's = 102,505,627 bp (20.32%) number of N's = 39,487 bp (0.01%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 2,065,042 number of insertions = 44,736 mapped reads with insertion percentage = 0.83% number of deletions = 54,282 mapped reads with deletion percentage = 1.01% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.163X std coverageData = 16.5506X There is a 2.51% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% 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 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 117238323 0.4703632132575509 31.701233585668856 chr2 243199373 25300737 0.10403290390061984 10.345364178223935 chr3 198022430 30073251 0.15186790203513814 10.28780512618147 chr4 191154276 10733262 0.05614973530594733 4.978323720430302 chr5 180915260 61472351 0.339785328224938 21.543002883766576 chr6 171115067 35928472 0.20996673542488226 16.31218917938545 chr7 159138663 9388809 0.05899766168074442 6.180520415600862 chr8 146364022 40970048 0.27991884508339077 28.136373672604655 chr9 141213431 6204663 0.0439381931028926 3.137609347809234 chr10 135534747 29171991 0.2152362522947713 29.29269402171579 chr11 135006516 9289134 0.06880507900818654 2.3064928257018518 chr12 133851895 7935531 0.05928590700938526 6.035344948265782 chr13 115169878 7463224 0.06480187467073639 7.375927181091065 chr14 107349540 16493677 0.153644598756548 9.204997064734245 chr15 102531392 3303894 0.03222324339456934 2.61567736968026 chr16 90354753 29412642 0.32552401532213804 27.273413919902 chr17 81195210 11353193 0.13982589613352808 16.347042643815215 chr18 78077248 12418698 0.1590565538375533 11.203807100049014 chr19 59128983 2258577 0.03819746062603512 0.9464075641621706 chr20 63025520 2217984 0.035191839749993334 1.2629945317183517 chr21 48129895 5031783 0.10454589605898787 13.516484477604216 chr22 51304566 6761802 0.13179727511972325 17.445751832890167 chrMT 16571 65363 3.944420976404562 2.906004510019635 chrX 155270560 24011093 0.15464034521418613 14.278911543250594 chrY 59373566 160161 0.0026975135702645855 0.18046121590330014