BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264614.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,055,213,826 number of mapped reads = 1,051,084,156 (99.61%) number of supplementary alignments = 12,747,785 (1.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 526,574,725 number of mapped paired reads (second in pair) = 524,509,431 number of mapped paired reads (both in pair) = 1,048,059,698 number of mapped paired reads (singletons) = 3,024,458 number of mapped bases = 104,397,187,863 bp number of sequenced bases = 104,373,550,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 306,536,503 duplication rate = 29.19% >>>>>>> Insert size mean insert size = 181,822.8724 std insert size = 4,077,857.8046 median insert size = 304 >>>>>>> Mapping quality mean mapping quality = 54.5176 >>>>>>> ACTG content number of A's = 32,311,004,820 bp (30.96%) number of C's = 19,770,528,431 bp (18.94%) number of T's = 32,226,809,803 bp (30.88%) number of G's = 20,014,307,106 bp (19.18%) number of N's = 50,900,808 bp (0.05%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 380,678,203 number of insertions = 10,704,197 mapped reads with insertion percentage = 1% number of deletions = 10,521,501 mapped reads with deletion percentage = 0.98% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 33.7234X std coverageData = 27.5108X There is a 90.79% of reference with a coverageData >= 1X There is a 89.48% of reference with a coverageData >= 2X There is a 88.15% of reference with a coverageData >= 3X There is a 86.79% of reference with a coverageData >= 4X There is a 85.42% of reference with a coverageData >= 5X There is a 84.04% of reference with a coverageData >= 6X There is a 82.65% of reference with a coverageData >= 7X There is a 81.26% of reference with a coverageData >= 8X There is a 79.86% of reference with a coverageData >= 9X There is a 78.45% of reference with a coverageData >= 10X There is a 77.04% of reference with a coverageData >= 11X There is a 75.62% of reference with a coverageData >= 12X There is a 74.2% of reference with a coverageData >= 13X There is a 72.77% of reference with a coverageData >= 14X There is a 71.34% of reference with a coverageData >= 15X There is a 69.91% of reference with a coverageData >= 16X There is a 68.47% of reference with a coverageData >= 17X There is a 67.04% of reference with a coverageData >= 18X There is a 65.6% of reference with a coverageData >= 19X There is a 64.16% of reference with a coverageData >= 20X There is a 62.73% of reference with a coverageData >= 21X There is a 61.29% of reference with a coverageData >= 22X There is a 59.86% of reference with a coverageData >= 23X There is a 58.43% of reference with a coverageData >= 24X There is a 57.01% of reference with a coverageData >= 25X There is a 55.59% of reference with a coverageData >= 26X There is a 54.17% of reference with a coverageData >= 27X There is a 52.76% of reference with a coverageData >= 28X There is a 51.35% of reference with a coverageData >= 29X There is a 49.96% of reference with a coverageData >= 30X There is a 48.57% of reference with a coverageData >= 31X There is a 47.19% of reference with a coverageData >= 32X There is a 45.82% of reference with a coverageData >= 33X There is a 44.46% of reference with a coverageData >= 34X There is a 43.12% of reference with a coverageData >= 35X There is a 41.78% of reference with a coverageData >= 36X There is a 40.47% of reference with a coverageData >= 37X There is a 39.17% of reference with a coverageData >= 38X There is a 37.89% of reference with a coverageData >= 39X There is a 36.62% of reference with a coverageData >= 40X There is a 35.38% of reference with a coverageData >= 41X There is a 34.15% of reference with a coverageData >= 42X There is a 32.95% of reference with a coverageData >= 43X There is a 31.77% of reference with a coverageData >= 44X There is a 30.62% of reference with a coverageData >= 45X There is a 29.49% of reference with a coverageData >= 46X There is a 28.38% of reference with a coverageData >= 47X There is a 27.3% of reference with a coverageData >= 48X There is a 26.24% of reference with a coverageData >= 49X There is a 25.21% of reference with a coverageData >= 50X There is a 24.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8008950338 32.132117889487624 28.18021013950227 chr2 243199373 9611977340 39.52303503677207 26.44983870496099 chr3 198022430 8217032781 41.49546483698842 25.982270267038864 chr4 191154276 8776156716 45.91138058559569 26.880153677543515 chr5 180915260 7604976648 42.03612590778688 26.32376858722425 chr6 171115067 6989501783 40.8467933627376 26.792704982974826 chr7 159138663 6084296518 38.23267333847087 28.816519479408765 chr8 146364022 5778891529 39.483005796328825 26.105182064134546 chr9 141213431 4364954645 30.910336319213148 29.02561277370451 chr10 135534747 4528203363 33.40990751987754 24.688847704602445 chr11 135006516 4786580938 35.454443828474176 27.322404236732435 chr12 133851895 4998417711 37.34289836539109 28.17508675670113 chr13 115169878 4477805436 38.88000503048202 29.804550545303815 chr14 107349540 3327720072 30.998922510520305 27.885537481468464 chr15 102531392 2751112611 26.831905403176425 26.498774865417026 chr16 90354753 1847226102 20.444149761551557 21.72209245866311 chr17 81195210 1565194150 19.27692717341331 20.703795051511367 chr18 78077248 3124603416 40.01938459716203 26.404121447795497 chr19 59128983 623210498 10.539848080931817 13.6125065873919 chr20 63025520 1546247213 24.533668472707564 26.17490148677906 chr21 48129895 1397944644 29.04524607834694 32.63874485466603 chr22 51304566 495780655 9.663480147166629 15.166719333815951 chrMT 16571 384819 23.222436787158287 7.083524461716754 chrX 155270560 3083600631 19.8595318455733 13.981838920105712 chrY 59373566 406417306 6.845088368113177 13.125386714877457