BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779298.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 44,505,720 number of mapped reads = 42,868,651 (96.32%) number of supplementary alignments = 107,395 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,551,879 number of mapped paired reads (second in pair) = 21,316,772 number of mapped paired reads (both in pair) = 42,565,564 number of mapped paired reads (singletons) = 303,087 number of mapped bases = 3,413,395,335 bp number of sequenced bases = 3,412,755,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,077,333 duplication rate = 6.63% >>>>>>> Insert size mean insert size = 36,377.6755 std insert size = 1,784,379.613 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 52.9647 >>>>>>> ACTG content number of A's = 1,051,540,502 bp (30.81%) number of C's = 650,554,943 bp (19.06%) number of T's = 1,046,439,604 bp (30.66%) number of G's = 663,311,439 bp (19.44%) number of N's = 909,485 bp (0.03%) GC percentage = 38.5% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 11,700,173 number of insertions = 245,338 mapped reads with insertion percentage = 0.57% number of deletions = 309,975 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 1.1026X std coverageData = 3.7726X There is a 27.47% of reference with a coverageData >= 1X There is a 16.68% of reference with a coverageData >= 2X There is a 11.55% of reference with a coverageData >= 3X There is a 8.59% of reference with a coverageData >= 4X There is a 6.65% of reference with a coverageData >= 5X There is a 5.3% of reference with a coverageData >= 6X There is a 4.31% of reference with a coverageData >= 7X There is a 3.57% of reference with a coverageData >= 8X There is a 2.99% of reference with a coverageData >= 9X There is a 2.53% of reference with a coverageData >= 10X There is a 2.16% of reference with a coverageData >= 11X There is a 1.86% of reference with a coverageData >= 12X There is a 1.62% of reference with a coverageData >= 13X There is a 1.41% of reference with a coverageData >= 14X There is a 1.24% of reference with a coverageData >= 15X There is a 1.09% of reference with a coverageData >= 16X There is a 0.97% of reference with a coverageData >= 17X There is a 0.86% of reference with a coverageData >= 18X There is a 0.77% of reference with a coverageData >= 19X There is a 0.69% of reference with a coverageData >= 20X There is a 0.62% of reference with a coverageData >= 21X There is a 0.56% of reference with a coverageData >= 22X There is a 0.51% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.42% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.35% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 203108759 0.8148776447782652 3.744574188793128 chr2 243199373 273026504 1.122644769318546 3.3544671726489836 chr3 198022430 232339885 1.1733008477877986 3.5580517598796138 chr4 191154276 225522015 1.179790584438718 3.367504886340481 chr5 180915260 195315655 1.0795974590534818 3.327520567715237 chr6 171115067 195533408 1.1427012911726822 3.715314682275742 chr7 159138663 333673759 2.0967485380972444 5.674520161074006 chr8 146364022 256384311 1.7516894349896999 4.541912431540742 chr9 141213431 115880103 0.82060256010634 2.8113525890003377 chr10 135534747 72275176 0.533259386244326 3.9150699741664634 chr11 135006516 175853597 1.3025563669830573 4.212089553706311 chr12 133851895 149523593 1.117082376756788 3.513204772269722 chr13 115169878 129382559 1.1234062347448175 3.4661886756382727 chr14 107349540 70574447 0.6574266363880087 2.591859241546762 chr15 102531392 85727826 0.8361129633351706 2.9955064151002118 chr16 90354753 66038454 0.7308796915199358 2.771452909235481 chr17 81195210 64765157 0.79764750900946 3.1147404976005726 chr18 78077248 85336733 1.092978238679724 3.7813337717754694 chr19 59128983 37136002 0.6280507479724453 2.5795709290289834 chr20 63025520 74555774 1.1829457971945332 3.608430333497282 chr21 48129895 50682789 1.053041752947934 3.5842973081285496 chr22 51304566 14732067 0.28714923736027703 1.1542430832678994 chrMT 16571 2410 0.14543479572747572 0.39049050202271224 chrX 155270560 301371401 1.940943608369803 5.822029306927277 chrY 59373566 4652951 0.07836738322235859 0.8809410978774515