BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779333.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 131,025,486 number of mapped reads = 126,308,150 (96.4%) number of supplementary alignments = 525,155 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 63,856,213 number of mapped paired reads (second in pair) = 62,451,937 number of mapped paired reads (both in pair) = 124,153,596 number of mapped paired reads (singletons) = 2,154,554 number of mapped bases = 12,526,530,104 bp number of sequenced bases = 12,523,592,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,679,530 duplication rate = 5.79% >>>>>>> Insert size mean insert size = 55,015.253 std insert size = 2,363,281.7101 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 53.9888 >>>>>>> ACTG content number of A's = 3,698,479,469 bp (29.53%) number of C's = 2,549,097,417 bp (20.35%) number of T's = 3,680,279,584 bp (29.39%) number of G's = 2,594,937,773 bp (20.72%) number of N's = 798,575 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 45,727,110 number of insertions = 1,320,076 mapped reads with insertion percentage = 1.03% number of deletions = 1,324,061 mapped reads with deletion percentage = 1.03% homopolymer indels = 48.2% >>>>>>> Coverage mean coverageData = 4.0464X std coverageData = 6.8896X There is a 79.8% of reference with a coverageData >= 1X There is a 65.8% of reference with a coverageData >= 2X There is a 52.55% of reference with a coverageData >= 3X There is a 41.34% of reference with a coverageData >= 4X There is a 32.35% of reference with a coverageData >= 5X There is a 25.32% of reference with a coverageData >= 6X There is a 19.89% of reference with a coverageData >= 7X There is a 15.71% of reference with a coverageData >= 8X There is a 12.49% of reference with a coverageData >= 9X There is a 9.99% of reference with a coverageData >= 10X There is a 8.04% of reference with a coverageData >= 11X There is a 6.51% of reference with a coverageData >= 12X There is a 5.31% of reference with a coverageData >= 13X There is a 4.35% of reference with a coverageData >= 14X There is a 3.59% of reference with a coverageData >= 15X There is a 2.97% of reference with a coverageData >= 16X There is a 2.48% of reference with a coverageData >= 17X There is a 2.08% of reference with a coverageData >= 18X There is a 1.75% of reference with a coverageData >= 19X There is a 1.48% of reference with a coverageData >= 20X There is a 1.26% of reference with a coverageData >= 21X There is a 1.07% of reference with a coverageData >= 22X There is a 0.92% of reference with a coverageData >= 23X There is a 0.79% of reference with a coverageData >= 24X There is a 0.68% of reference with a coverageData >= 25X There is a 0.59% of reference with a coverageData >= 26X There is a 0.51% of reference with a coverageData >= 27X There is a 0.45% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.34% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% 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 1111324973 4.458664811109939 6.92086924035233 chr2 243199373 1115963042 4.588675654192579 17.093854842489204 chr3 198022430 905370500 4.5720603469011065 5.018320533853698 chr4 191154276 738396631 3.862830831992479 4.454179494921985 chr5 180915260 805534279 4.4525502105239765 4.872664436210852 chr6 171115067 727613863 4.252190504065899 4.692330889396766 chr7 159138663 617681570 3.881404797274186 4.639589638316529 chr8 146364022 627911247 4.2900655394670695 4.85730025651631 chr9 141213431 516078765 3.6546011335139927 4.914625025916352 chr10 135534747 717743192 5.295639737314004 6.549018745332727 chr11 135006516 636880332 4.717404395503399 5.25744901233369 chr12 133851895 596844169 4.458989310536096 5.695214388542768 chr13 115169878 345247700 2.997725672679796 3.997086348336317 chr14 107349540 371565316 3.4612660287133044 4.3549312107883456 chr15 102531392 380036603 3.706538998319656 4.753302869231584 chr16 90354753 308036029 3.409184561657758 4.3455455566088865 chr17 81195210 354861343 4.370471398497522 5.383762605303314 chr18 78077248 310789565 3.9805394396072975 4.9958954314605055 chr19 59128983 205707904 3.4789690869535166 5.221357728656556 chr20 63025520 263938904 4.187810017275542 5.000328770194581 chr21 48129895 145896507 3.0313074026028937 5.076192760300115 chr22 51304566 151695312 2.956760456759346 4.789676102602158 chrMT 16571 1879740 113.43551988413493 26.861774174383942 chrX 155270560 560552375 3.6101652174114656 4.331443041337709 chrY 59373566 8980243 0.15124985081744963 1.6983160745240833