BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778442.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 = 457,417,538 number of mapped reads = 413,507,277 (90.4%) number of supplementary alignments = 947,544 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 207,618,664 number of mapped paired reads (second in pair) = 205,888,613 number of mapped paired reads (both in pair) = 402,976,804 number of mapped paired reads (singletons) = 10,530,473 number of mapped bases = 40,954,252,449 bp number of sequenced bases = 40,940,935,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,252,485 duplication rate = 8.71% >>>>>>> Insert size mean insert size = 49,750.9383 std insert size = 2,176,576.4548 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 53.5664 >>>>>>> ACTG content number of A's = 12,064,340,724 bp (29.47%) number of C's = 8,424,981,566 bp (20.58%) number of T's = 11,993,775,648 bp (29.3%) number of G's = 8,453,059,626 bp (20.65%) number of N's = 4,777,654 bp (0.01%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 221,581,702 number of insertions = 4,439,404 mapped reads with insertion percentage = 1.04% number of deletions = 5,658,573 mapped reads with deletion percentage = 1.33% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 13.2294X std coverageData = 128.9662X There is a 91.71% of reference with a coverageData >= 1X There is a 91.63% of reference with a coverageData >= 2X There is a 91.51% of reference with a coverageData >= 3X There is a 91.28% of reference with a coverageData >= 4X There is a 90.81% of reference with a coverageData >= 5X There is a 89.87% of reference with a coverageData >= 6X There is a 88.19% of reference with a coverageData >= 7X There is a 85.47% of reference with a coverageData >= 8X There is a 81.44% of reference with a coverageData >= 9X There is a 76.01% of reference with a coverageData >= 10X There is a 69.25% of reference with a coverageData >= 11X There is a 61.45% of reference with a coverageData >= 12X There is a 53.03% of reference with a coverageData >= 13X There is a 44.48% of reference with a coverageData >= 14X There is a 36.29% of reference with a coverageData >= 15X There is a 28.83% of reference with a coverageData >= 16X There is a 22.34% of reference with a coverageData >= 17X There is a 16.93% of reference with a coverageData >= 18X There is a 12.58% of reference with a coverageData >= 19X There is a 9.21% of reference with a coverageData >= 20X There is a 6.67% of reference with a coverageData >= 21X There is a 4.81% of reference with a coverageData >= 22X There is a 3.46% of reference with a coverageData >= 23X There is a 2.51% of reference with a coverageData >= 24X There is a 1.85% of reference with a coverageData >= 25X There is a 1.38% of reference with a coverageData >= 26X There is a 1.06% of reference with a coverageData >= 27X There is a 0.84% of reference with a coverageData >= 28X There is a 0.68% of reference with a coverageData >= 29X There is a 0.57% of reference with a coverageData >= 30X There is a 0.49% of reference with a coverageData >= 31X There is a 0.44% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.33% of reference with a coverageData >= 35X There is a 0.31% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.27% of reference with a coverageData >= 39X There is a 0.26% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3270242916 13.120299973094149 321.53490630447254 chr2 243199373 3391926582 13.947102495202568 85.06744284438147 chr3 198022430 2625728149 13.259751175662272 11.55948908603974 chr4 191154276 2639215308 13.806729115492033 111.97374578536994 chr5 180915260 2380363452 13.15733925374786 12.850947628632799 chr6 171115067 2275665002 13.299033462669888 52.54557488701509 chr7 159138663 2169457125 13.632495611704366 138.69870800681034 chr8 146364022 1976815815 13.50615942352281 134.77468882912234 chr9 141213431 1707960549 12.094887411948797 147.9528358710715 chr10 135534747 2490184386 18.373033049598714 200.00825578864638 chr11 135006516 1822149029 13.496748771740766 49.98025691519579 chr12 133851895 2198655756 16.42603383388782 17.534259961179313 chr13 115169878 1256454489 10.909575583643495 8.183727942849826 chr14 107349540 1191841543 11.102437355576932 11.771760091442188 chr15 102531392 1119326685 10.916916889219644 9.776424103166237 chr16 90354753 1224624689 13.553517090572978 64.82593473486301 chr17 81195210 1119837529 13.791916161064181 51.28258608079972 chr18 78077248 1082451003 13.863846776464252 149.24978557319338 chr19 59128983 825325119 13.95804691922403 150.58475508095077 chr20 63025520 832890897 13.2151372491651 27.576921449300233 chr21 48129895 551905575 11.467001434347614 41.68517388927569 chr22 51304566 493570358 9.620398270204644 11.722880174279979 chrMT 16571 168050444 10141.23734234506 916.7209380668278 chrX 155270560 2009858683 12.944235423637295 31.76797156554489 chrY 59373566 129751366 2.1853389435965496 108.05821352362925