BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751170.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 7,871,480 number of mapped reads = 7,822,051 (99.37%) number of supplementary alignments = 68,627 (0.87%) number of secondary alignments = 0 number of mapped bases = 1,029,167,405 bp number of sequenced bases = 1,028,846,878 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,274,809 duplication rate = 14.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.5956 >>>>>>> ACTG content number of A's = 309,698,284 bp (30.1%) number of C's = 205,112,935 bp (19.94%) number of T's = 310,020,522 bp (30.13%) number of G's = 203,984,549 bp (19.83%) number of N's = 30,588 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0168 number of mismatches = 17,050,602 number of insertions = 116,866 mapped reads with insertion percentage = 1.47% number of deletions = 194,261 mapped reads with deletion percentage = 2.41% homopolymer indels = 41.02% >>>>>>> Coverage mean coverageData = 0.3325X std coverageData = 1.8025X There is a 11.59% of reference with a coverageData >= 1X There is a 5.85% of reference with a coverageData >= 2X There is a 3.51% of reference with a coverageData >= 3X There is a 2.35% of reference with a coverageData >= 4X There is a 1.69% of reference with a coverageData >= 5X There is a 1.27% of reference with a coverageData >= 6X There is a 0.98% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.63% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 120999992 0.48545512751199926 1.9391120470743086 chr2 243199373 80736086 0.3319748937017202 2.1631320511960013 chr3 198022430 80547728 0.40676062807632446 2.0589551347193797 chr4 191154276 62976338 0.32945293883983007 1.888086540279833 chr5 180915260 99025767 0.5473599463085645 2.0838129563949472 chr6 171115067 63886295 0.3733528328046063 1.6734383758020646 chr7 159138663 58627128 0.36840279348080235 2.1021748462686958 chr8 146364022 51152383 0.3494874102325502 1.5532770287611974 chr9 141213431 39281933 0.27817419860013176 1.3071076947332723 chr10 135534747 45865458 0.3384036862517624 1.6915035092617703 chr11 135006516 46183607 0.342084281324614 2.238402052021779 chr12 133851895 59442603 0.4440923529696759 2.335636004233701 chr13 115169878 41912966 0.363922986876829 2.490519208644765 chr14 107349540 22339483 0.20810040732358984 1.3116599158861115 chr15 102531392 16967603 0.1654869076584857 1.0631151398686334 chr16 90354753 16028665 0.17739703189714878 1.2847490641590764 chr17 81195210 8557954 0.10539973971370971 0.6637945469687097 chr18 78077248 29404230 0.37660433421014017 1.7063771337496056 chr19 59128983 4358605 0.07371351203520615 0.6761941500492206 chr20 63025520 12871176 0.2042216549740486 0.9879818376136048 chr21 48129895 15850951 0.32933691212083466 1.6837948796926485 chr22 51304566 2885769 0.0562478006343529 0.4450269877617498 chrMT 16571 1110 0.06698449097821495 0.27962051050746717 chrX 155270560 48666577 0.3134308074885542 1.592872900660398 chrY 59373566 596998 0.010054946000716885 0.27032531723817965