BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779286.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 = 9,775,538 number of mapped reads = 9,523,375 (97.42%) number of supplementary alignments = 24,104 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,805,663 number of mapped paired reads (second in pair) = 4,717,712 number of mapped paired reads (both in pair) = 9,422,466 number of mapped paired reads (singletons) = 100,909 number of mapped bases = 757,908,760 bp number of sequenced bases = 757,763,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,240 duplication rate = 1.26% >>>>>>> Insert size mean insert size = 47,347.2854 std insert size = 2,050,979.3292 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.1188 >>>>>>> ACTG content number of A's = 232,155,782 bp (30.64%) number of C's = 145,840,652 bp (19.25%) number of T's = 231,249,476 bp (30.52%) number of G's = 148,373,848 bp (19.58%) number of N's = 143,378 bp (0.02%) GC percentage = 38.83% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 3,017,075 number of insertions = 55,238 mapped reads with insertion percentage = 0.57% number of deletions = 70,216 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.2448X std coverageData = 0.8107X There is a 14.76% of reference with a coverageData >= 1X There is a 5.08% of reference with a coverageData >= 2X There is a 2.13% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 54196188 0.21743652145203682 0.8154784748612935 chr2 243199373 62689428 0.2577696941677559 0.7654602089017767 chr3 198022430 56860256 0.28714048201509296 0.8067583463515998 chr4 191154276 65360174 0.3419236826279523 0.8915805300787554 chr5 180915260 48434715 0.26772045100009806 0.7968297047820649 chr6 171115067 46728773 0.27308391843717655 0.8113035599239986 chr7 159138663 52581926 0.3304157833725171 1.179280217935787 chr8 146364022 55122959 0.37661549776214814 0.965606982721733 chr9 141213431 30455376 0.21566911719608314 0.7736200484380054 chr10 135534747 19937266 0.14710077261589605 0.8910784460182887 chr11 135006516 33528241 0.248345353938324 0.7646413977139614 chr12 133851895 34106160 0.25480520839843174 0.7637631265390364 chr13 115169878 21793804 0.18923180590674935 0.6634166405175983 chr14 107349540 22664866 0.21113146828575138 0.7005364905602701 chr15 102531392 19711441 0.19224786297644336 0.6670292812326095 chr16 90354753 12524620 0.13861606151477168 0.5322852524121243 chr17 81195210 14117320 0.1738688772404185 0.642226755871485 chr18 78077248 19409447 0.24859286792485308 0.7587669125828255 chr19 59128983 7444831 0.12590832147408995 0.5945965524445151 chr20 63025520 16502270 0.26183472980468864 0.793669832500651 chr21 48129895 8493563 0.17647167108924713 0.6210461032192641 chr22 51304566 4374906 0.08527322889740457 0.4269641083535285 chrMT 16571 720 0.04344939955343673 0.2387681398944592 chrX 155270560 50324800 0.32411037868350573 0.9883266020933936 chrY 59373566 544710 0.009174284731356713 0.1396902120822452