BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068147.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,584,358 number of mapped reads = 4,390,705 (95.78%) number of supplementary alignments = 31,629 (0.69%) number of secondary alignments = 0 number of mapped bases = 290,042,564 bp number of sequenced bases = 289,907,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 511,921 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8321 >>>>>>> ACTG content number of A's = 78,144,203 bp (26.95%) number of C's = 52,283,027 bp (18.03%) number of T's = 94,015,063 bp (32.43%) number of G's = 65,430,889 bp (22.57%) number of N's = 34,311 bp (0.01%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,591,156 number of insertions = 19,047 mapped reads with insertion percentage = 0.43% number of deletions = 75,731 mapped reads with deletion percentage = 1.71% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.0937X std coverageData = 0.8814X There is a 6.89% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 32195893 0.129170763430114 2.1057338804989567 chr2 243199373 25914179 0.10655528704837573 1.0349360325804313 chr3 198022430 17856800 0.09017564323395082 0.3849235353879981 chr4 191154276 15592555 0.08157052683456581 0.40371939828979947 chr5 180915260 13541743 0.07485130331183781 0.35130732879204357 chr6 171115067 22071894 0.12898860624587782 0.5931686060662229 chr7 159138663 22395460 0.14072922052889184 0.9521143024511703 chr8 146364022 9862922 0.0673862460543753 1.1248633028844957 chr9 141213431 9529430 0.06748246206127517 0.6495740931942954 chr10 135534747 16838056 0.12423423788144895 0.69872864194988 chr11 135006516 12270566 0.09088869458715608 0.5411375078500823 chr12 133851895 11460918 0.08562387555290121 0.4013525619676134 chr13 115169878 7817698 0.06787971070004954 0.3509143854645053 chr14 107349540 5769871 0.05374844643023156 0.3520765533529089 chr15 102531392 5287437 0.051568957534488556 0.3343639162604512 chr16 90354753 6312775 0.06986655145856024 0.387747664312594 chr17 81195210 8747023 0.10772831303718532 0.4571135849384221 chr18 78077248 7133171 0.09136043063403054 1.2133110876994533 chr19 59128983 6288852 0.10635819662245839 1.3521602650700497 chr20 63025520 4750626 0.0753762285499588 0.38504979235049824 chr21 48129895 4860144 0.10097973411327825 0.44175768118190467 chr22 51304566 3263838 0.0636169108223233 0.3164605732865278 chrMT 16571 186597 11.260455011767545 6.5388209618844675 chrX 155270560 19275418 0.12414084163797696 0.5584671409794998 chrY 59373566 818698 0.013788930919190538 0.4089720814277885