BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004112.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 = 2,924,606 number of mapped reads = 2,281,146 (78%) number of supplementary alignments = 12,341 (0.42%) number of secondary alignments = 0 number of mapped bases = 145,074,000 bp number of sequenced bases = 144,998,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,073 duplication rate = 7.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9257 >>>>>>> ACTG content number of A's = 37,870,187 bp (26.12%) number of C's = 25,486,516 bp (17.58%) number of T's = 48,297,381 bp (33.31%) number of G's = 33,326,230 bp (22.98%) number of N's = 18,137 bp (0.01%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,486,692 number of insertions = 11,555 mapped reads with insertion percentage = 0.5% number of deletions = 46,311 mapped reads with deletion percentage = 2.01% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.0469X std coverageData = 0.4194X There is a 3.42% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 13088302 0.052510609391821735 0.6916250602726915 chr2 243199373 12155689 0.04998240270956619 0.5114142467042209 chr3 198022430 9246360 0.046693498307237215 0.2818177909796888 chr4 191154276 10999122 0.05754054907984376 0.3225036969664357 chr5 180915260 8903554 0.049213946905308045 0.29064172934686405 chr6 171115067 10166723 0.05941454004164344 0.3722281058524198 chr7 159138663 8003253 0.05029106597433208 0.6024024098844032 chr8 146364022 8709774 0.05950761588117604 0.5105931832120326 chr9 141213431 5449873 0.03859316328062307 0.3766472305757972 chr10 135534747 6393669 0.047173652082000785 0.36086788754302035 chr11 135006516 6322796 0.046833265440314006 0.4128638107237719 chr12 133851895 5749746 0.04295602987167272 0.2759862594333979 chr13 115169878 4140679 0.03595279487923049 0.24722507235242475 chr14 107349540 3878295 0.036127728167256234 0.26703153590634876 chr15 102531392 3995469 0.03896825081629634 0.26113784564952053 chr16 90354753 3839283 0.04249121238812971 0.288491262343939 chr17 81195210 3365629 0.0414510782101555 0.28874850935140217 chr18 78077248 3869668 0.04956204399007506 0.7092706764104214 chr19 59128983 2184254 0.03694049667656215 0.46892546345066455 chr20 63025520 3944387 0.06258396598711126 0.3402861571500939 chr21 48129895 1986485 0.04127341229395992 0.27988731297783637 chr22 51304566 1245597 0.024278482347945406 0.2006480048751339 chrMT 16571 150943 9.108864884436667 6.24443167715546 chrX 155270560 6944828 0.044727268324400965 0.31774790632125677 chrY 59373566 339622 0.005720087622832019 0.12563159428343765