BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779086.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 = 5,829,940 number of mapped reads = 5,645,628 (96.84%) number of supplementary alignments = 31,160 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,846,200 number of mapped paired reads (second in pair) = 2,799,428 number of mapped paired reads (both in pair) = 5,577,656 number of mapped paired reads (singletons) = 67,972 number of mapped bases = 563,744,971 bp number of sequenced bases = 563,616,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,029 duplication rate = 1.33% >>>>>>> Insert size mean insert size = 65,506.3997 std insert size = 2,469,791.5442 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.6449 >>>>>>> ACTG content number of A's = 170,906,092 bp (30.32%) number of C's = 110,369,171 bp (19.58%) number of T's = 170,067,438 bp (30.17%) number of G's = 112,082,520 bp (19.89%) number of N's = 191,729 bp (0.03%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 2,572,537 number of insertions = 47,106 mapped reads with insertion percentage = 0.82% number of deletions = 57,523 mapped reads with deletion percentage = 1% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.1821X std coverageData = 0.62X There is a 12.6% of reference with a coverageData >= 1X There is a 3.79% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% 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 43753135 0.17553872012218577 0.7733768876529374 chr2 243199373 45458094 0.1869169868295672 0.606843208854385 chr3 198022430 38318077 0.19350372076536987 0.5782939019375167 chr4 191154276 39887648 0.20866730702900937 0.6004797871121345 chr5 180915260 36513241 0.20182510308970067 0.5804085774927694 chr6 171115067 30322863 0.17720744018409554 0.5503016693994838 chr7 159138663 48312749 0.30358900903924274 0.998777280910981 chr8 146364022 40147293 0.27429755244085874 0.688790341011096 chr9 141213431 24580431 0.17406581531185938 0.5737836864738446 chr10 135534747 12043660 0.08886031269900109 0.6496995612770387 chr11 135006516 26485700 0.19618090137219749 0.5816235175202381 chr12 133851895 22190908 0.16578702901441925 0.5337893177042767 chr13 115169878 18816963 0.163384413761383 0.530266783632974 chr14 107349540 17535501 0.16334956814905774 0.5371558770883812 chr15 102531392 13458326 0.13126054116187166 0.4709830679769241 chr16 90354753 13564756 0.15012775254888916 0.5015305350700731 chr17 81195210 9960754 0.1226766209484525 0.46471574638545304 chr18 78077248 13114407 0.1679670753764272 0.5469527036282669 chr19 59128983 7199373 0.12175709161106323 0.580151130468672 chr20 63025520 13497547 0.2141600259704323 0.6028227345003615 chr21 48129895 6563809 0.13637696487806591 0.48403408004780074 chr22 51304566 3679871 0.07172599413471308 0.33570430635950355 chrMT 16571 1398 0.08436425079958965 0.28921210407431386 chrX 155270560 37941367 0.24435647684918507 0.6619655100504829 chrY 59373566 397100 0.006688161529661197 0.12387052898224125