BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779425.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 = 16,574,366 number of mapped reads = 16,236,161 (97.96%) number of supplementary alignments = 66,419 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,184,473 number of mapped paired reads (second in pair) = 8,051,688 number of mapped paired reads (both in pair) = 16,074,622 number of mapped paired reads (singletons) = 161,539 number of mapped bases = 1,291,479,853 bp number of sequenced bases = 1,291,205,781 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 659,949 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 34,785.0717 std insert size = 1,757,992.7117 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.1938 >>>>>>> ACTG content number of A's = 390,661,123 bp (30.26%) number of C's = 253,591,013 bp (19.64%) number of T's = 389,847,478 bp (30.19%) number of G's = 256,820,957 bp (19.89%) number of N's = 285,210 bp (0.02%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,315,796 number of insertions = 116,025 mapped reads with insertion percentage = 0.71% number of deletions = 133,395 mapped reads with deletion percentage = 0.81% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.4172X std coverageData = 1.7615X There is a 18.42% of reference with a coverageData >= 1X There is a 9.36% of reference with a coverageData >= 2X There is a 5.15% of reference with a coverageData >= 3X There is a 3.03% of reference with a coverageData >= 4X There is a 1.86% of reference with a coverageData >= 5X There is a 1.18% of reference with a coverageData >= 6X There is a 0.76% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% 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 113209718 0.4542003448007457 3.821003689946322 chr2 243199373 74840729 0.30773405406764764 1.0705741255004844 chr3 198022430 125927169 0.6359237637877689 1.4840264387546527 chr4 191154276 84729720 0.4432530716707588 1.2409590508768868 chr5 180915260 111886960 0.6184495437256095 1.4470082623051872 chr6 171115067 82755937 0.4836274119566572 1.356730687122032 chr7 159138663 171613930 1.0783924331449235 2.7123184849144706 chr8 146364022 83029783 0.5672827370103289 1.4918983647234867 chr9 141213431 62624431 0.443473616896965 1.370854669329052 chr10 135534747 28161446 0.20778026759440515 2.355913920630369 chr11 135006516 30745667 0.22773468948713557 0.8840331813642296 chr12 133851895 17541787 0.1310537067853989 0.6162306420886056 chr13 115169878 52010817 0.4516008691091954 1.530164432329358 chr14 107349540 19799128 0.18443607676381288 0.797308633505601 chr15 102531392 26575266 0.25919150692892184 0.9485590174459438 chr16 90354753 18179774 0.2012044014994983 0.7953759517037448 chr17 81195210 25409482 0.31294311573305866 1.1420044530892357 chr18 78077248 17951972 0.2299257781216879 1.1633090358151674 chr19 59128983 17913822 0.3029617810270811 2.24839966197384 chr20 63025520 20503648 0.3253229485452877 1.0690777516962264 chr21 48129895 20953500 0.4353531209656701 1.2085845547828586 chr22 51304566 10056670 0.19601900540392447 0.752737491562903 chrMT 16571 160 0.00965542212298594 0.09778647629714904 chrX 155270560 68728673 0.44263814724439715 1.2969090118457596 chrY 59373566 6329664 0.10660744210647546 0.5973057416598591