BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,792,089 number of mapped reads = 2,630,899 (94.23%) number of supplementary alignments = 17,362 (0.62%) number of secondary alignments = 0 number of mapped bases = 171,974,477 bp number of sequenced bases = 171,878,286 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 247,173 duplication rate = 7.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2771 >>>>>>> ACTG content number of A's = 44,181,882 bp (25.71%) number of C's = 31,951,322 bp (18.59%) number of T's = 54,622,205 bp (31.78%) number of G's = 41,106,699 bp (23.92%) number of N's = 16,178 bp (0.01%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,275,946 number of insertions = 15,784 mapped reads with insertion percentage = 0.59% number of deletions = 56,647 mapped reads with deletion percentage = 2.13% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.8483X There is a 4.52% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 18453682 0.07403665405511668 1.8324169011307767 chr2 243199373 13457995 0.05533729315987998 0.9016392348847092 chr3 198022430 21840429 0.11029270270039611 0.4213124816942546 chr4 191154276 5403853 0.02826958995152167 0.2662262272087019 chr5 180915260 7384872 0.04081950853675914 0.24526104482047884 chr6 171115067 8463511 0.04946093379374944 0.4047414076009077 chr7 159138663 18477484 0.11610933290296652 1.8594105300134849 chr8 146364022 8644981 0.05906493195438425 0.6799147973720544 chr9 141213431 6200465 0.04390846505244958 0.4873943671449009 chr10 135534747 8455226 0.062384194364563945 0.9216939500526137 chr11 135006516 6820419 0.050519183829616045 0.46311071887691857 chr12 133851895 3295635 0.024621504237948965 0.20727467875039143 chr13 115169878 8838680 0.07674471965664495 0.34445625031955096 chr14 107349540 6307408 0.058755799046740206 0.36276557230956064 chr15 102531392 2918631 0.028465730768582564 0.23958372472883457 chr16 90354753 4744137 0.05250567172708667 0.37529854507265004 chr17 81195210 4018509 0.049491946630841895 0.32789660987387426 chr18 78077248 3337776 0.042749662488104086 1.3479634770064162 chr19 59128983 4897441 0.08282640342385053 1.1198320783592424 chr20 63025520 3213998 0.05099518417301436 0.36057376148347736 chr21 48129895 2319686 0.0481963652735997 0.2973505973225761 chr22 51304566 1160624 0.022622236001372666 0.17253787139740473 chrMT 16571 127117 7.671051837547523 7.810998540565515 chrX 155270560 2755208 0.017744561493176814 0.27762197642149655 chrY 59373566 436710 0.007355293431423674 0.2140635805033344