BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251075.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 3,227,322 number of mapped reads = 3,076,122 (95.32%) number of supplementary alignments = 25,838 (0.8%) number of secondary alignments = 0 number of mapped bases = 239,563,552 bp number of sequenced bases = 239,426,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 685,591 duplication rate = 19.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1208 >>>>>>> ACTG content number of A's = 69,830,714 bp (29.17%) number of C's = 47,595,583 bp (19.88%) number of T's = 71,016,343 bp (29.66%) number of G's = 50,965,072 bp (21.29%) number of N's = 18,878 bp (0.01%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,406,796 number of insertions = 29,241 mapped reads with insertion percentage = 0.93% number of deletions = 76,338 mapped reads with deletion percentage = 2.44% homopolymer indels = 45.4% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 0.927X There is a 5.09% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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% 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 19369938 0.07771269705281898 1.9408724385037337 chr2 243199373 18454504 0.07588220221274995 1.016754162097966 chr3 198022430 15780230 0.0796891039060575 0.4007254269434944 chr4 191154276 15250098 0.07977900530982629 0.49125183898335345 chr5 180915260 14457482 0.07991300457462792 0.41299802390897167 chr6 171115067 13598470 0.07946974067456024 0.519555588002303 chr7 159138663 13396577 0.0841817867980957 1.4210968827654116 chr8 146364022 11760774 0.08035290257328402 0.6164693137332613 chr9 141213431 10032866 0.07104753371511807 1.1916445172906385 chr10 135534747 14303106 0.10553091599455304 0.9833219314441213 chr11 135006516 10840830 0.08029856870019518 0.5496646842000505 chr12 133851895 10736352 0.08021068360668335 0.4115515919673605 chr13 115169878 7415802 0.06439011770074116 0.3528217719415511 chr14 107349540 7295677 0.06796188414035123 0.6297247589752835 chr15 102531392 6689039 0.06523893677362734 0.35559429879562204 chr16 90354753 6940266 0.07681129956716277 0.6416058018126609 chr17 81195210 6250853 0.07698548966127436 0.5333696912558628 chr18 78077248 6468495 0.08284737443614816 1.1500487226025085 chr19 59128983 4884847 0.08261341142972135 1.850921726573686 chr20 63025520 5014924 0.07956973619575054 0.4608037929413288 chr21 48129895 3163862 0.0657359007327982 0.44060312663148343 chr22 51304566 2675892 0.05215699514932063 0.33178692269379545 chrMT 16571 243489 14.69368173314827 8.962574538600403 chrX 155270560 13720816 0.08836714442196898 0.503684329757645 chrY 59373566 818363 0.013783288677658337 0.7560703658026181