BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779091.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 = 32,738,126 number of mapped reads = 31,380,333 (95.85%) number of supplementary alignments = 168,143 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,921,624 number of mapped paired reads (second in pair) = 15,458,709 number of mapped paired reads (both in pair) = 30,806,840 number of mapped paired reads (singletons) = 573,493 number of mapped bases = 3,135,089,315 bp number of sequenced bases = 3,134,346,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,419,080 duplication rate = 3.88% >>>>>>> Insert size mean insert size = 79,920.5571 std insert size = 2,789,734.4507 median insert size = 279 >>>>>>> Mapping quality mean mapping quality = 53.379 >>>>>>> ACTG content number of A's = 958,139,116 bp (30.57%) number of C's = 605,238,336 bp (19.31%) number of T's = 954,499,481 bp (30.45%) number of G's = 615,427,011 bp (19.63%) number of N's = 1,042,740 bp (0.03%) GC percentage = 38.94% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 15,293,327 number of insertions = 273,279 mapped reads with insertion percentage = 0.86% number of deletions = 332,628 mapped reads with deletion percentage = 1.04% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 1.0127X std coverageData = 3.1662X There is a 32.22% of reference with a coverageData >= 1X There is a 18.95% of reference with a coverageData >= 2X There is a 12.29% of reference with a coverageData >= 3X There is a 8.46% of reference with a coverageData >= 4X There is a 6.06% of reference with a coverageData >= 5X There is a 4.47% of reference with a coverageData >= 6X There is a 3.37% of reference with a coverageData >= 7X There is a 2.59% of reference with a coverageData >= 8X There is a 2.02% of reference with a coverageData >= 9X There is a 1.59% of reference with a coverageData >= 10X There is a 1.27% of reference with a coverageData >= 11X There is a 1.02% of reference with a coverageData >= 12X There is a 0.83% of reference with a coverageData >= 13X There is a 0.68% of reference with a coverageData >= 14X There is a 0.56% of reference with a coverageData >= 15X There is a 0.47% of reference with a coverageData >= 16X There is a 0.4% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 291412723 1.169155454180393 3.534208284612955 chr2 243199373 314947885 1.295019313228246 3.0635104920825524 chr3 198022430 297856172 1.504153706224088 3.0606273999243507 chr4 191154276 140216903 0.7335274205427662 2.0521050552964635 chr5 180915260 234950277 1.298675838621905 2.7872426874304432 chr6 171115067 223906560 1.308514579841178 2.844078506335548 chr7 159138663 243184531 1.5281297857831067 7.833499752253279 chr8 146364022 232341359 1.5874212516515842 2.967550047571943 chr9 141213431 99980369 0.7080089216159616 2.029679062434639 chr10 135534747 51401398 0.379248857859306 3.6633688542712286 chr11 135006516 112568597 0.8338012144539749 2.0987460498371537 chr12 133851895 123727447 0.9243608168565712 2.392486308234687 chr13 115169878 99369697 0.8628097791333946 2.200278677582319 chr14 107349540 126505935 1.1784487851554837 2.8186211485022534 chr15 102531392 83396669 0.8133769314279865 2.3636640524595087 chr16 90354753 44685057 0.49455126062931076 1.5767045394328796 chr17 81195210 38625423 0.4757106115003582 1.7760911382704188 chr18 78077248 49034513 0.6280256317435778 1.9314533206306534 chr19 59128983 19954102 0.3374673635093639 1.7220680692507113 chr20 63025520 74348190 1.1796521472571746 2.495444961006384 chr21 48129895 29492053 0.6127595541191186 1.8245744730206137 chr22 51304566 12708876 0.24771432624534823 1.0992315422929728 chrMT 16571 855 0.051596161969706116 0.23624878053088327 chrX 155270560 188689694 1.2152316189237677 2.928063612704999 chrY 59373566 1784030 0.030047546748329046 0.5170336368763749