BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068071.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 = 4,838,550 number of mapped reads = 4,555,290 (94.15%) number of supplementary alignments = 41,088 (0.85%) number of secondary alignments = 0 number of mapped bases = 292,239,673 bp number of sequenced bases = 292,129,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 963,031 duplication rate = 15.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1231 >>>>>>> ACTG content number of A's = 74,920,933 bp (25.65%) number of C's = 53,294,305 bp (18.24%) number of T's = 94,636,367 bp (32.4%) number of G's = 69,245,020 bp (23.7%) number of N's = 33,362 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,668,990 number of insertions = 19,257 mapped reads with insertion percentage = 0.42% number of deletions = 63,156 mapped reads with deletion percentage = 1.37% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.0944X std coverageData = 1.0975X There is a 5.33% of reference with a coverageData >= 1X There is a 2.13% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 36088097 0.14478638751315287 2.141800353299158 chr2 243199373 26261895 0.10798504402394163 2.1838864964045546 chr3 198022430 13304058 0.06718460125956438 0.4164426433880007 chr4 191154276 15469211 0.08092526792338142 0.5407792131656518 chr5 180915260 14966706 0.08272771462175164 0.46866086620094827 chr6 171115067 17443532 0.10194036273848404 0.8080959391030732 chr7 159138663 19832152 0.12462183372748331 1.1589952397903232 chr8 146364022 12708151 0.08682564763080916 1.027832782685286 chr9 141213431 9416232 0.06668085275826206 0.749750160589862 chr10 135534747 14290954 0.10544125632964069 0.7534708966845303 chr11 135006516 14499376 0.10739760146095467 0.7102121798801265 chr12 133851895 13362089 0.09982741746017118 0.5446125670063288 chr13 115169878 8668039 0.07526307356164778 0.5339172124915731 chr14 107349540 7087367 0.0660214007437759 0.4846727803895085 chr15 102531392 8155391 0.0795404299202336 0.5131713958468959 chr16 90354753 6287543 0.06958729664171624 0.47856279644284794 chr17 81195210 8763356 0.10792947022367452 0.5786741575238293 chr18 78077248 9332577 0.11953004542373215 1.5001915337460503 chr19 59128983 5239482 0.08861106236175244 1.295013648569974 chr20 63025520 3971030 0.06300669950838962 0.4435667332781694 chr21 48129895 6063758 0.1259873515202973 0.6211950937068085 chr22 51304566 4487625 0.0874702848085685 0.4713249785011214 chrMT 16571 310361 18.729165409450243 13.869917263147816 chrX 155270560 15309273 0.09859739669902652 0.6179236536474239 chrY 59373566 921418 0.015518993755571293 0.7245393111894839