BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779156.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 = 6,135,270 number of mapped reads = 5,926,619 (96.6%) number of supplementary alignments = 34,397 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,981,790 number of mapped paired reads (second in pair) = 2,944,829 number of mapped paired reads (both in pair) = 5,863,908 number of mapped paired reads (singletons) = 62,711 number of mapped bases = 591,953,235 bp number of sequenced bases = 591,813,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,056 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 73,043.9368 std insert size = 2,604,701.5649 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 53.6187 >>>>>>> ACTG content number of A's = 180,355,392 bp (30.48%) number of C's = 114,975,457 bp (19.43%) number of T's = 179,278,266 bp (30.29%) number of G's = 116,963,622 bp (19.76%) number of N's = 240,658 bp (0.04%) GC percentage = 39.19% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 2,565,597 number of insertions = 50,149 mapped reads with insertion percentage = 0.83% number of deletions = 62,095 mapped reads with deletion percentage = 1.03% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.1912X std coverageData = 0.6888X There is a 13.67% of reference with a coverageData >= 1X There is a 3.69% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 47892547 0.1921461491564348 0.8283626234346091 chr2 243199373 47923136 0.19705287644799974 0.6078992734633466 chr3 198022430 39020275 0.1970497736039296 0.5433748648511835 chr4 191154276 42693962 0.22334819232607697 0.5928074496660185 chr5 180915260 38199419 0.2111453671735596 0.5644313738679105 chr6 171115067 32421929 0.18947442541690382 0.5444044067475481 chr7 159138663 60091226 0.37760293361268216 1.5610154658831887 chr8 146364022 44730923 0.3056141966363838 0.6972781370784401 chr9 141213431 21447616 0.15188085048369088 0.510132766953666 chr10 135534747 11730427 0.08654922268752234 0.9737227105686366 chr11 135006516 28624572 0.21202363299264756 0.5731059704479524 chr12 133851895 19987780 0.14932758329644866 0.4775892784683418 chr13 115169878 24150204 0.2096920168657294 0.580048683860292 chr14 107349540 16665078 0.1552412613971145 0.4930752480801419 chr15 102531392 16580175 0.16170827954817973 0.5163726645598051 chr16 90354753 11167624 0.1235975267399602 0.4336159059425893 chr17 81195210 9480694 0.11676420320853903 0.44543414141415383 chr18 78077248 15018427 0.19235343694490872 0.556753790988472 chr19 59128983 7380043 0.12481261516031825 0.5558883381086661 chr20 63025520 13848636 0.2197306107113436 0.6000235752404864 chr21 48129895 6941278 0.14421967885032785 0.47558800563463516 chr22 51304566 3431865 0.06689199943724307 0.31781573312808015 chrMT 16571 238 0.014362440407941584 0.11897966512589414 chrX 155270560 32113142 0.20682054601979924 0.5844187475228932 chrY 59373566 412019 0.006939434966732502 0.12558509904815046