BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549093.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,526,871 number of mapped reads = 10,063,453 (87.3%) number of secondary alignments = 0 number of mapped bases = 399,221,282 bp number of sequenced bases = 399,186,157 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 488,203 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.865 >>>>>>> ACTG content number of A's = 119,415,398 bp (29.91%) number of C's = 80,105,324 bp (20.07%) number of T's = 121,074,028 bp (30.33%) number of G's = 78,490,337 bp (19.66%) number of N's = 101,070 bp (0.03%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,698,514 number of insertions = 10,272 mapped reads with insertion percentage = 0.1% number of deletions = 28,523 mapped reads with deletion percentage = 0.28% homopolymer indels = 43.59% >>>>>>> Coverage mean coverageData = 0.129X std coverageData = 1.6839X There is a 10.67% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 33059806 0.13263680494501154 4.687282107346952 chr2 243199373 34157033 0.14044868857453838 1.0906371859072703 chr3 198022430 29288779 0.14790637101059714 0.4771486998142075 chr4 191154276 28121891 0.14711620157531816 0.4724783189776899 chr5 180915260 26078286 0.1441464141830822 0.4929949705396609 chr6 171115067 24546654 0.14345115500553787 0.6241433468371791 chr7 159138663 21904271 0.13764267329555233 1.5776809013245185 chr8 146364022 22463366 0.15347600928867614 1.4260045988413694 chr9 141213431 16975091 0.12020875691349783 1.0808214377938399 chr10 135534747 18708851 0.13803730345252352 1.4526497084986043 chr11 135006516 18100458 0.13407099550661689 0.9897334126061984 chr12 133851895 18102937 0.1352460269613665 0.5310654841507936 chr13 115169878 13770304 0.11956515227011007 0.3824958413845327 chr14 107349540 12231225 0.11393830844547634 0.6146329558340663 chr15 102531392 10376760 0.10120568732744797 0.36583765678779717 chr16 90354753 10334609 0.11437814455649058 0.7030496093166252 chr17 81195210 9911382 0.12206855552193288 0.5088254992051819 chr18 78077248 11124833 0.1424849528507972 2.358059594052736 chr19 59128983 6228208 0.10533257438234647 3.7308383008263157 chr20 63025520 7759722 0.12312031697636132 0.4481426896333761 chr21 48129895 5210632 0.10826186094941616 0.5313281616152336 chr22 51304566 3525773 0.0687224018228709 0.36943659454550554 chrMT 16571 39122 2.3608714018465995 2.8466116632358256 chrX 155270560 13942729 0.08979634645485918 0.617225942072277 chrY 59373566 3258560 0.05488233602138703 0.44000277463515014