BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779391.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 = 8,758,082 number of mapped reads = 5,605,233 (64%) number of supplementary alignments = 47,301 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,836,732 number of mapped paired reads (second in pair) = 2,768,501 number of mapped paired reads (both in pair) = 5,461,518 number of mapped paired reads (singletons) = 143,715 number of mapped bases = 442,073,058 bp number of sequenced bases = 441,977,667 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,252,088 duplication rate = 10% >>>>>>> Insert size mean insert size = 89,563.9887 std insert size = 2,727,486.5264 median insert size = 327 >>>>>>> Mapping quality mean mapping quality = 51.2583 >>>>>>> ACTG content number of A's = 139,027,132 bp (31.46%) number of C's = 77,976,336 bp (17.64%) number of T's = 131,242,533 bp (29.69%) number of G's = 93,641,716 bp (21.19%) number of N's = 89,950 bp (0.02%) GC percentage = 38.83% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 3,415,498 number of insertions = 46,718 mapped reads with insertion percentage = 0.83% number of deletions = 49,433 mapped reads with deletion percentage = 0.87% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.1428X std coverageData = 4.4221X There is a 5.43% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 35200089 0.14122367622907547 5.072964417254945 chr2 243199373 39965978 0.16433421479256857 5.094869518599766 chr3 198022430 30175491 0.15238420718299436 2.4424982402038906 chr4 191154276 34963378 0.18290659634524734 3.2736535982713613 chr5 180915260 43521884 0.24056502475247252 6.386042603529573 chr6 171115067 18852607 0.11017502625879227 3.8036260325841056 chr7 159138663 51172724 0.3215606002672022 7.740723023614268 chr8 146364022 24361747 0.16644628008377632 4.116131247915662 chr9 141213431 12018772 0.0851106861074709 3.29634859443267 chr10 135534747 11037343 0.08143552295117355 2.868196673837957 chr11 135006516 15587976 0.11546091597534448 1.270448956965526 chr12 133851895 20883025 0.15601590847854638 4.812385108368301 chr13 115169878 14675874 0.12742805892353207 1.5595557487955858 chr14 107349540 12016712 0.11194004184833954 2.3176067919305567 chr15 102531392 14166968 0.1381720049211855 8.751355982883672 chr16 90354753 8683923 0.09610919970087241 5.801330926232632 chr17 81195210 8299781 0.10222008170186395 4.979573398838914 chr18 78077248 10402748 0.13323661202812886 2.666184192993967 chr19 59128983 4090087 0.06917228730282744 2.1360457690017878 chr20 63025520 5582784 0.0885797372239055 2.391938025860041 chr21 48129895 7447280 0.15473293677453484 4.006164381841898 chr22 51304566 1751097 0.03413140654966266 0.5209453410402083 chrMT 16571 98636 5.952326353267757 4.508561460323843 chrX 155270560 14543081 0.0936628360199126 2.513016150085038 chrY 59373566 2573073 0.04333701297307964 0.5208562322507527