BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779212.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 = 14,303,602 number of mapped reads = 13,986,131 (97.78%) number of supplementary alignments = 33,986 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,032,924 number of mapped paired reads (second in pair) = 6,953,207 number of mapped paired reads (both in pair) = 13,889,898 number of mapped paired reads (singletons) = 96,233 number of mapped bases = 1,113,309,062 bp number of sequenced bases = 1,113,105,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 173,845 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 46,054.4666 std insert size = 2,006,656.9832 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.9183 >>>>>>> ACTG content number of A's = 341,239,930 bp (30.66%) number of C's = 213,957,097 bp (19.22%) number of T's = 340,498,035 bp (30.59%) number of G's = 217,197,321 bp (19.51%) number of N's = 212,641 bp (0.02%) GC percentage = 38.73% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,169,254 number of insertions = 79,522 mapped reads with insertion percentage = 0.56% number of deletions = 99,433 mapped reads with deletion percentage = 0.7% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.3596X std coverageData = 0.9376X There is a 22.24% of reference with a coverageData >= 1X There is a 7.86% of reference with a coverageData >= 2X There is a 3.05% of reference with a coverageData >= 3X There is a 1.31% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 75783804 0.3040466005498939 0.9702346593997923 chr2 243199373 72865986 0.2996142017191796 0.7434630862749969 chr3 198022430 77693737 0.39234816480133083 0.8585235257186906 chr4 191154276 94308257 0.4933620056712726 0.9739351191583571 chr5 180915260 80044233 0.44244047185406027 0.9182378666804596 chr6 171115067 66483557 0.38853128579261814 0.8663213030115785 chr7 159138663 93544039 0.5878146594709043 1.687522615856728 chr8 146364022 94120023 0.6430543634555219 1.1539786211977068 chr9 141213431 45041541 0.3189607438969456 0.8281641406254953 chr10 135534747 24351379 0.1796689006989477 1.132367507393328 chr11 135006516 48413394 0.35860042488615884 0.8517836703921843 chr12 133851895 52345741 0.3910720950196484 0.8699336215189523 chr13 115169878 38264814 0.332246718191366 0.7813373861474843 chr14 107349540 33432691 0.3114376736034453 0.796462677192089 chr15 102531392 25955183 0.25314376888592327 0.7105791199257134 chr16 90354753 20898092 0.2312893489952875 0.650207191700094 chr17 81195210 18582694 0.22886441207553992 0.6723947178092531 chr18 78077248 28344813 0.3630355029931383 0.8283521378187709 chr19 59128983 11670984 0.1973817814522533 0.7042680676902412 chr20 63025520 22316019 0.35407909367507 0.8648743856757727 chr21 48129895 11702466 0.24314339351872677 0.679733189993507 chr22 51304566 6420400 0.12514285765520364 0.47207579626030954 chrMT 16571 1209 0.0729587834168125 0.36376795840639525 chrX 155270560 69839431 0.44979184077136064 0.9715068047156843 chrY 59373566 884575 0.01489846508461358 0.17562755271216834