BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779426.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 = 12,767,828 number of mapped reads = 12,024,161 (94.18%) number of supplementary alignments = 105,812 (0.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,069,494 number of mapped paired reads (second in pair) = 5,954,667 number of mapped paired reads (both in pair) = 11,861,516 number of mapped paired reads (singletons) = 162,645 number of mapped bases = 953,427,948 bp number of sequenced bases = 953,220,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,471,168 duplication rate = 12.16% >>>>>>> Insert size mean insert size = 157,538.3925 std insert size = 3,778,482.3227 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 51.9848 >>>>>>> ACTG content number of A's = 298,982,751 bp (31.37%) number of C's = 178,154,394 bp (18.69%) number of T's = 292,995,558 bp (30.74%) number of G's = 182,880,189 bp (19.19%) number of N's = 207,949 bp (0.02%) GC percentage = 37.88% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 3,842,573 number of insertions = 95,857 mapped reads with insertion percentage = 0.79% number of deletions = 106,591 mapped reads with deletion percentage = 0.88% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.308X std coverageData = 12.6824X There is a 6.57% of reference with a coverageData >= 1X There is a 3.24% of reference with a coverageData >= 2X There is a 2.08% of reference with a coverageData >= 3X There is a 1.51% of reference with a coverageData >= 4X There is a 1.17% of reference with a coverageData >= 5X There is a 0.95% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.67% of reference with a coverageData >= 8X There is a 0.58% of reference with a coverageData >= 9X There is a 0.5% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.17% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.14% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.12% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 73592306 0.2952542533484801 14.832130535163122 chr2 243199373 76613211 0.3150222389759204 6.470463166993434 chr3 198022430 74009256 0.37374178268593106 10.246599263387917 chr4 191154276 68404360 0.35784896593158083 4.226293495149145 chr5 180915260 87041490 0.48111745797452354 10.474317373612053 chr6 171115067 34667727 0.20259891550052692 3.924699360073518 chr7 159138663 128537277 0.8077061512072651 27.121199211531223 chr8 146364022 42241695 0.28860709362031606 5.133793056492385 chr9 141213431 32524028 0.23031823368132737 3.5324517185199733 chr10 135534747 28315821 0.20891927440569907 6.806445042388774 chr11 135006516 36033691 0.26690334709474317 11.774744826779509 chr12 133851895 45509098 0.3399959186233411 10.601592313139506 chr13 115169878 45254869 0.39294014881217465 27.57194941605245 chr14 107349540 27439288 0.25560694531154954 9.879573831838092 chr15 102531392 18359518 0.17906240851582314 3.0109478226338275 chr16 90354753 13429049 0.14862581717200865 3.2099476629623998 chr17 81195210 10454022 0.12875170838279745 1.6413514909032711 chr18 78077248 44255377 0.5668152776081452 24.00501486769723 chr19 59128983 12835019 0.21706815082545897 18.194102008084702 chr20 63025520 9687131 0.15370172273072877 1.3790341536191832 chr21 48129895 8051370 0.16728417961435402 1.3287835806977957 chr22 51304566 2601674 0.05071037926721766 0.895563086364801 chrMT 16571 72511 4.375776959748959 2.8340679609839454 chrX 155270560 25594563 0.16483847936144494 13.726226582518407 chrY 59373566 7903597 0.1331164276034894 22.19494109942003