BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779200.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 = 8,043,210 number of mapped reads = 7,782,477 (96.76%) number of supplementary alignments = 25,384 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,939,159 number of mapped paired reads (second in pair) = 3,843,318 number of mapped paired reads (both in pair) = 7,670,736 number of mapped paired reads (singletons) = 111,741 number of mapped bases = 618,349,871 bp number of sequenced bases = 618,219,828 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,320 duplication rate = 0.64% >>>>>>> Insert size mean insert size = 49,020.4996 std insert size = 2,136,783.3037 median insert size = 268 >>>>>>> Mapping quality mean mapping quality = 53.2317 >>>>>>> ACTG content number of A's = 185,747,260 bp (30.05%) number of C's = 122,136,018 bp (19.76%) number of T's = 185,246,829 bp (29.96%) number of G's = 124,977,847 bp (20.22%) number of N's = 111,874 bp (0.02%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 3,062,542 number of insertions = 52,728 mapped reads with insertion percentage = 0.67% number of deletions = 63,684 mapped reads with deletion percentage = 0.81% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.1997X std coverageData = 0.8712X There is a 15.56% of reference with a coverageData >= 1X There is a 3.25% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 43516154 0.17458794616202783 1.9977223796362757 chr2 243199373 47672303 0.19602148809816217 0.5556627617136894 chr3 198022430 50736822 0.2562175507087758 0.5782901485164171 chr4 191154276 34164844 0.17872916429031385 0.49482311463007383 chr5 180915260 29141814 0.16107991111418682 0.4549898322948641 chr6 171115067 42246896 0.2468917363074755 0.6441279524541429 chr7 159138663 46737919 0.2936930480558329 0.9778026652844836 chr8 146364022 57423244 0.3923316892726547 0.7424437344319015 chr9 141213431 25374712 0.1796904998363789 0.6411625340836532 chr10 135534747 15370755 0.1134082243869168 1.5400213200799913 chr11 135006516 24342260 0.18030433434783252 0.507467999948264 chr12 133851895 24291675 0.18148174144265944 0.4941752867057251 chr13 115169878 20898916 0.1814616491996284 0.48964344873015936 chr14 107349540 20011243 0.18641200511897862 0.504318663247535 chr15 102531392 21105660 0.20584583500046502 0.532915676279671 chr16 90354753 16881952 0.1868407741649186 0.5145507205048419 chr17 81195210 10833682 0.13342759997788048 0.7064828124437904 chr18 78077248 19829443 0.2539721046520492 0.7529209506473742 chr19 59128983 11456523 0.19375477843074013 1.2713741260259257 chr20 63025520 15895094 0.25220091797735267 0.5963917210213466 chr21 48129895 6737764 0.13999124660463108 0.4436119284546915 chr22 51304566 4447220 0.08668273307291986 0.345626353901415 chrMT 16571 657 0.039647577092511016 0.19512982017929606 chrX 155270560 28765755 0.18526213211313208 0.4953472376263127 chrY 59373566 466564 0.007858109785758868 0.11630766372533115