BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781911.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 = 43,514,672 number of mapped reads = 42,745,456 (98.23%) number of supplementary alignments = 180,545 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,553,450 number of mapped paired reads (second in pair) = 21,192,006 number of mapped paired reads (both in pair) = 42,258,566 number of mapped paired reads (singletons) = 486,890 number of mapped bases = 4,240,715,566 bp number of sequenced bases = 4,239,675,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,313,527 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 58,103.1992 std insert size = 2,322,271.0862 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 53.9171 >>>>>>> ACTG content number of A's = 1,273,898,619 bp (30.05%) number of C's = 841,339,168 bp (19.84%) number of T's = 1,271,818,002 bp (30%) number of G's = 851,878,535 bp (20.09%) number of N's = 740,931 bp (0.02%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 15,624,271 number of insertions = 481,188 mapped reads with insertion percentage = 1.11% number of deletions = 466,641 mapped reads with deletion percentage = 1.07% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 1.3699X std coverageData = 2.0504X There is a 57.26% of reference with a coverageData >= 1X There is a 33.72% of reference with a coverageData >= 2X There is a 19.14% of reference with a coverageData >= 3X There is a 10.85% of reference with a coverageData >= 4X There is a 6.21% of reference with a coverageData >= 5X There is a 3.62% of reference with a coverageData >= 6X There is a 2.15% of reference with a coverageData >= 7X There is a 1.31% of reference with a coverageData >= 8X There is a 0.82% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 325572405 1.3062049903578776 2.2873032648789247 chr2 243199373 343195295 1.411168502478006 2.7564703268570327 chr3 198022430 290187524 1.4654275477782996 1.8222368317414839 chr4 191154276 272108330 1.4235011410364684 1.8387564882306466 chr5 180915260 252764611 1.3971436737840688 1.7542526639931313 chr6 171115067 246928497 1.443055257080313 1.8575403187529065 chr7 159138663 215882090 1.3565659402328898 1.8356864493793503 chr8 146364022 210804028 1.4402721728977903 1.819014407142267 chr9 141213431 172066589 1.218486002227366 1.9559238335419677 chr10 135534747 229559579 1.6937323017248116 2.5824997772865568 chr11 135006516 190378410 1.4101423815721605 1.8344041194513503 chr12 133851895 279211312 2.085972051422955 2.551275422471938 chr13 115169878 128032185 1.1116811723982203 1.5923130232958205 chr14 107349540 122979709 1.1456007077440666 1.6948905172719084 chr15 102531392 114286428 1.11464816551013 1.7091742641324188 chr16 90354753 144537089 1.5996622667985159 2.1985348270310197 chr17 81195210 89306546 1.0998991935608025 1.6808424590516926 chr18 78077248 104442681 1.3376839434709584 1.8804806606221893 chr19 59128983 58218187 0.9845964541619124 1.8377024661545056 chr20 63025520 79641154 1.2636334297598815 1.9104628016792373 chr21 48129895 47333461 0.983452405204707 1.9259217102318775 chr22 51304566 37009435 0.7213672755754332 1.388568781144364 chrMT 16571 150669 9.092329974051053 3.8344512903122845 chrX 155270560 282445580 1.819054301085795 2.197225691593909 chrY 59373566 3673772 0.061875549129051806 0.6852762000174217