BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779399.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 = 17,008,884 number of mapped reads = 15,985,391 (93.98%) number of supplementary alignments = 74,795 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,054,378 number of mapped paired reads (second in pair) = 7,931,013 number of mapped paired reads (both in pair) = 15,813,578 number of mapped paired reads (singletons) = 171,813 number of mapped bases = 1,269,532,341 bp number of sequenced bases = 1,269,247,092 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 985,000 duplication rate = 4.94% >>>>>>> Insert size mean insert size = 42,541.7646 std insert size = 1,942,332.2773 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.8352 >>>>>>> ACTG content number of A's = 388,804,300 bp (30.63%) number of C's = 243,876,145 bp (19.21%) number of T's = 387,139,553 bp (30.5%) number of G's = 249,144,653 bp (19.63%) number of N's = 282,441 bp (0.02%) GC percentage = 38.84% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,749,697 number of insertions = 120,596 mapped reads with insertion percentage = 0.75% number of deletions = 138,717 mapped reads with deletion percentage = 0.86% homopolymer indels = 46.79% >>>>>>> Coverage mean coverageData = 0.4101X std coverageData = 3.01X There is a 16.54% of reference with a coverageData >= 1X There is a 8.13% of reference with a coverageData >= 2X There is a 4.52% of reference with a coverageData >= 3X There is a 2.81% of reference with a coverageData >= 4X There is a 1.86% of reference with a coverageData >= 5X There is a 1.3% of reference with a coverageData >= 6X There is a 0.94% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.54% of reference with a coverageData >= 9X There is a 0.43% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 86968280 0.34891901031612677 7.3452317196529355 chr2 243199373 103160909 0.42418246283883304 1.6851037085655358 chr3 198022430 105149968 0.531000291229635 1.6922480455048308 chr4 191154276 94345986 0.49355938027773966 1.4899260850636833 chr5 180915260 124128728 0.6861153006109048 1.9748001835047084 chr6 171115067 72245925 0.4222066838801518 2.202179176120081 chr7 159138663 128593182 0.808057448616368 3.339639107499745 chr8 146364022 68286464 0.46655225148158336 1.65980816723075 chr9 141213431 92553231 0.6554137970063202 3.6263338133280234 chr10 135534747 18918851 0.13958672162497193 4.752874543736051 chr11 135006516 58364744 0.4323105708468175 1.6990848534272245 chr12 133851895 46428752 0.3468666020753759 1.542344264723704 chr13 115169878 33368656 0.289734230681394 1.4599928368580029 chr14 107349540 24525660 0.2284654410256439 1.5383061433087966 chr15 102531392 27686529 0.2700297778069764 1.1449487922724289 chr16 90354753 32222581 0.3566229769893787 1.6002824820972046 chr17 81195210 21598178 0.2660031053555992 1.8337036255967751 chr18 78077248 27156690 0.3478182274047364 2.317989625814192 chr19 59128983 12984806 0.21960137552171327 4.555334165471117 chr20 63025520 19337243 0.3068160802163949 1.4481770119917037 chr21 48129895 17291996 0.35927765892695174 1.5035393292327393 chr22 51304566 7356649 0.14339170123766373 1.842816357095877 chrMT 16571 108243 6.532074105364794 3.554673789225407 chrX 155270560 39796442 0.2563038479412968 1.1062971598969855 chrY 59373566 6953648 0.1171169001370071 1.281742779583901