BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1768994.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 = 437,047,566 number of mapped reads = 404,470,374 (92.55%) number of supplementary alignments = 1,215,829 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 203,903,649 number of mapped paired reads (second in pair) = 200,566,725 number of mapped paired reads (both in pair) = 397,115,080 number of mapped paired reads (singletons) = 7,355,294 number of mapped bases = 40,211,774,072 bp number of sequenced bases = 40,198,992,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,260,898 duplication rate = 8.38% >>>>>>> Insert size mean insert size = 48,292.0468 std insert size = 2,100,962.7112 median insert size = 270 >>>>>>> Mapping quality mean mapping quality = 53.5456 >>>>>>> ACTG content number of A's = 11,711,645,832 bp (29.13%) number of C's = 8,363,516,323 bp (20.81%) number of T's = 11,733,908,566 bp (29.19%) number of G's = 8,379,950,631 bp (20.85%) number of N's = 9,970,742 bp (0.02%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 230,413,850 number of insertions = 4,455,249 mapped reads with insertion percentage = 1.07% number of deletions = 5,330,762 mapped reads with deletion percentage = 1.28% homopolymer indels = 43.35% >>>>>>> Coverage mean coverageData = 12.9896X std coverageData = 143.0543X There is a 91.67% of reference with a coverageData >= 1X There is a 91.5% of reference with a coverageData >= 2X There is a 91.17% of reference with a coverageData >= 3X There is a 90.52% of reference with a coverageData >= 4X There is a 89.38% of reference with a coverageData >= 5X There is a 87.56% of reference with a coverageData >= 6X There is a 84.85% of reference with a coverageData >= 7X There is a 81.1% of reference with a coverageData >= 8X There is a 76.22% of reference with a coverageData >= 9X There is a 70.23% of reference with a coverageData >= 10X There is a 63.32% of reference with a coverageData >= 11X There is a 55.79% of reference with a coverageData >= 12X There is a 48.03% of reference with a coverageData >= 13X There is a 40.43% of reference with a coverageData >= 14X There is a 33.32% of reference with a coverageData >= 15X There is a 26.96% of reference with a coverageData >= 16X There is a 21.47% of reference with a coverageData >= 17X There is a 16.87% of reference with a coverageData >= 18X There is a 13.12% of reference with a coverageData >= 19X There is a 10.12% of reference with a coverageData >= 20X There is a 7.76% of reference with a coverageData >= 21X There is a 5.93% of reference with a coverageData >= 22X There is a 4.52% of reference with a coverageData >= 23X There is a 3.43% of reference with a coverageData >= 24X There is a 2.62% of reference with a coverageData >= 25X There is a 2% of reference with a coverageData >= 26X There is a 1.54% of reference with a coverageData >= 27X There is a 1.2% of reference with a coverageData >= 28X There is a 0.95% of reference with a coverageData >= 29X There is a 0.77% of reference with a coverageData >= 30X There is a 0.63% of reference with a coverageData >= 31X There is a 0.54% of reference with a coverageData >= 32X There is a 0.47% of reference with a coverageData >= 33X There is a 0.42% of reference with a coverageData >= 34X There is a 0.38% of reference with a coverageData >= 35X There is a 0.35% of reference with a coverageData >= 36X There is a 0.33% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.28% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3128137788 12.550170488843035 388.7807117555718 chr2 243199373 3285213481 13.50831394207583 111.41052926238076 chr3 198022430 2478570880 12.516616829719744 10.455744049440465 chr4 191154276 2445626873 12.79399511314097 75.21298864558118 chr5 180915260 2272180544 12.55936367114637 10.583436517910185 chr6 171115067 2044241942 11.946592300957343 46.884247052489954 chr7 159138663 3705254373 23.283181491854055 169.69260988693676 chr8 146364022 2731146045 18.659954869236923 140.5602508691066 chr9 141213431 1553438637 11.00064367814985 138.8762614971418 chr10 135534747 1148398865 8.473095574524516 205.95881614553625 chr11 135006516 1742472472 12.90658053867563 48.93682488279592 chr12 133851895 1672222575 12.493081065456712 12.543284941472535 chr13 115169878 1169495866 10.154528999327411 8.52588605471692 chr14 107349540 1151941389 10.73075291240186 14.335057451057958 chr15 102531392 1078473528 10.518471533089105 9.018607419116698 chr16 90354753 1204945640 13.335719483401167 73.61945137516128 chr17 81195210 1085677364 13.371199655743238 70.64945639938432 chr18 78077248 1032781152 13.227683844594523 144.73952124946288 chr19 59128983 1062373091 17.96704487543782 163.92696905268286 chr20 63025520 1175973450 18.658686989016513 22.496609154647484 chr21 48129895 517865689 10.759751065320213 37.011332954859924 chr22 51304566 474905666 9.256596498643026 9.77125105713635 chrMT 16571 8626342 520.5685836702673 58.518535480516206 chrX 155270560 1927190781 12.411823471236273 32.024966104952526 chrY 59373566 114619639 1.930482649467273 82.52272617095345