BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006221.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 12,089,438 number of mapped reads = 10,748,598 (88.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,423,412 number of mapped paired reads (second in pair) = 5,325,186 number of mapped paired reads (both in pair) = 9,911,728 number of mapped paired reads (singletons) = 836,870 number of mapped bases = 415,825,170 bp number of sequenced bases = 415,773,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 621,514 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 73,359.317 std insert size = 2,595,029.2219 median insert size = 136 >>>>>>> Mapping quality mean mapping quality = 48.2515 >>>>>>> ACTG content number of A's = 116,730,290 bp (28.08%) number of C's = 88,956,411 bp (21.4%) number of T's = 118,965,898 bp (28.61%) number of G's = 91,103,177 bp (21.91%) number of N's = 17,458 bp (0%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,649,744 number of insertions = 11,640 mapped reads with insertion percentage = 0.11% number of deletions = 39,241 mapped reads with deletion percentage = 0.37% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.1343X std coverageData = 0.6945X There is a 10.3% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 34710744 0.13926041131107153 1.0792089275107675 chr2 243199373 35100194 0.1443268276847079 0.6431069088477606 chr3 198022430 27665555 0.13970919859937078 0.4583231495522151 chr4 191154276 26021596 0.1361287675301598 0.5329246402156943 chr5 180915260 24861419 0.13742024304638537 0.4538033996488559 chr6 171115067 23415833 0.13684261363144604 0.5238687246512258 chr7 159138663 22041605 0.1385056565418047 0.808865553427633 chr8 146364022 20661211 0.1411631814818535 1.4308205932498523 chr9 141213431 17124482 0.12126666619976112 0.5464039018647112 chr10 135534747 19460681 0.14358444185534208 0.7418731721388703 chr11 135006516 19201735 0.1422282091925104 0.6087013687574572 chr12 133851895 19072557 0.14249000359688593 0.4694991631825814 chr13 115169878 13099581 0.11374138123164461 0.4111527454430936 chr14 107349540 12875776 0.1199425353848745 0.5026327610547763 chr15 102531392 11656386 0.11368602115535503 0.4116451055275112 chr16 90354753 12933054 0.14313639925505633 0.6499371538991356 chr17 81195210 11889049 0.14642549726763437 0.5034594500320412 chr18 78077248 10935625 0.14006160924114539 0.9620159270695717 chr19 59128983 8650952 0.1463064568521329 0.7633805655871914 chr20 63025520 8936959 0.14179905219346067 0.48543795812258006 chr21 48129895 5610403 0.11656794597204087 0.5189781218121646 chr22 51304566 5451028 0.10624839902163874 0.41428928459950615 chrMT 16571 52124 3.1454951421157444 2.6780462916705146 chrX 155270560 23330779 0.15025887070929608 0.5363665120736473 chrY 59373566 1065842 0.017951456713918783 0.40848980936084184