BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781912.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 = 47,066,032 number of mapped reads = 45,239,265 (96.12%) number of supplementary alignments = 163,356 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,873,472 number of mapped paired reads (second in pair) = 22,365,793 number of mapped paired reads (both in pair) = 44,434,592 number of mapped paired reads (singletons) = 804,673 number of mapped bases = 4,484,626,589 bp number of sequenced bases = 4,483,512,245 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,277,077 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 63,975.1401 std insert size = 2,471,111.5594 median insert size = 295 >>>>>>> Mapping quality mean mapping quality = 54.0302 >>>>>>> ACTG content number of A's = 1,337,497,865 bp (29.83%) number of C's = 898,581,446 bp (20.04%) number of T's = 1,335,495,427 bp (29.79%) number of G's = 911,150,578 bp (20.32%) number of N's = 786,929 bp (0.02%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 20,689,992 number of insertions = 523,457 mapped reads with insertion percentage = 1.14% number of deletions = 504,024 mapped reads with deletion percentage = 1.09% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 1.4487X std coverageData = 2.1874X There is a 60.18% of reference with a coverageData >= 1X There is a 35.52% of reference with a coverageData >= 2X There is a 20.21% of reference with a coverageData >= 3X There is a 11.48% of reference with a coverageData >= 4X There is a 6.61% of reference with a coverageData >= 5X There is a 3.89% of reference with a coverageData >= 6X There is a 2.35% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 0.93% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 380970603 1.5284640073173579 2.283810987190632 chr2 243199373 373907105 1.5374509415367612 3.7649509016586142 chr3 198022430 307081796 1.5507424891210557 1.8824499033121889 chr4 191154276 273541535 1.430998776088064 1.8095008873268192 chr5 180915260 269987115 1.4923401983890137 1.8200167099980147 chr6 171115067 260438409 1.522007462966426 1.9182681842814688 chr7 159138663 226508052 1.4233376586807192 1.8606337549662666 chr8 146364022 223063551 1.524032668356162 1.88207533443382 chr9 141213431 179463077 1.2708640794939683 1.8945778338702228 chr10 135534747 243952099 1.7999229304644662 2.5278392805129855 chr11 135006516 209381103 1.5508962767397094 1.923588978971279 chr12 133851895 305734742 2.2841271092949413 2.868539899042907 chr13 115169878 119923616 1.0412758794447972 1.5157552037639344 chr14 107349540 133004355 1.2389839304388264 1.7546536613545611 chr15 102531392 130921184 1.2768887795846955 1.8340115981945704 chr16 90354753 154251799 1.7071796876031524 2.2070842911866375 chr17 81195210 107941630 1.3294088407431917 1.7786502709029142 chr18 78077248 99784216 1.278019122805148 1.7358788715227047 chr19 59128983 66299983 1.1212772423297048 1.8919244106748554 chr20 63025520 84268930 1.3370604478947576 1.8888721589643356 chr21 48129895 48162578 1.0006790582028071 1.779870492466946 chr22 51304566 43936178 0.8563794887184115 1.5331495207547403 chrMT 16571 93288 5.629593868806952 2.9229024989477708 chrX 155270560 239135681 1.540122486838458 1.8838292190385746 chrY 59373566 2873964 0.04840477326222919 0.5665361073677586