BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779083.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 = 26,135,572 number of mapped reads = 25,337,863 (96.95%) number of supplementary alignments = 143,197 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,770,614 number of mapped paired reads (second in pair) = 12,567,249 number of mapped paired reads (both in pair) = 25,038,572 number of mapped paired reads (singletons) = 299,291 number of mapped bases = 2,527,707,012 bp number of sequenced bases = 2,527,133,373 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 822,139 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 76,777.3223 std insert size = 2,657,100.5012 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.5614 >>>>>>> ACTG content number of A's = 772,488,009 bp (30.57%) number of C's = 489,711,757 bp (19.38%) number of T's = 764,846,622 bp (30.27%) number of G's = 499,235,727 bp (19.76%) number of N's = 851,258 bp (0.03%) GC percentage = 39.13% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 11,691,321 number of insertions = 211,169 mapped reads with insertion percentage = 0.82% number of deletions = 256,532 mapped reads with deletion percentage = 0.99% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.8165X std coverageData = 2.1238X There is a 33.01% of reference with a coverageData >= 1X There is a 18.29% of reference with a coverageData >= 2X There is a 10.51% of reference with a coverageData >= 3X There is a 6.44% of reference with a coverageData >= 4X There is a 4.08% of reference with a coverageData >= 5X There is a 2.67% of reference with a coverageData >= 6X There is a 1.8% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.86% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% 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 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 206160622 0.8271217988259295 3.2137154700901727 chr2 243199373 221503150 0.910788326744576 2.0516278984177245 chr3 198022430 161854866 0.8173562257568499 1.737221195387794 chr4 191154276 186814780 0.9772984623163753 1.9057791449302535 chr5 180915260 149288812 0.8251863994225805 1.6949127896217515 chr6 171115067 169983973 0.9933898632082468 1.9601212390862182 chr7 159138663 171091347 1.0751086114126773 2.58617569896711 chr8 146364022 163551072 1.1174267402955078 1.9984801913694206 chr9 141213431 95984510 0.6797123284965719 1.8220508757073113 chr10 135534747 84878072 0.6262458438056479 3.681725770659777 chr11 135006516 96438234 0.7143228109078824 1.5762747867425948 chr12 133851895 107662388 0.8043396621317913 1.7827209658912335 chr13 115169878 97499049 0.8465672682226858 1.7449708518560276 chr14 107349540 88377666 0.8232700950558335 1.8226731538235963 chr15 102531392 61435640 0.5991885880179995 1.5540319102139082 chr16 90354753 44093385 0.4880029388160687 1.2855446404028923 chr17 81195210 50423912 0.6210207720381535 1.7070899789212919 chr18 78077248 64826771 0.8302901634033003 1.875232884229715 chr19 59128983 23788256 0.4023112658643224 2.066353746653997 chr20 63025520 45888378 0.7280920173288534 1.532904977077416 chr21 48129895 29124311 0.6051189390710285 1.4971684767448854 chr22 51304566 12882620 0.2511008474372437 0.8629885745645689 chrMT 16571 2088 0.1260032587049665 0.4447751649296616 chrX 155270560 192107082 1.237240865235496 2.3413155928110885 chrY 59373566 2046028 0.03446025121684623 0.43230214807477096