BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716633.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 4,249,167 number of mapped reads = 2,304,421 (54.23%) number of supplementary alignments = 11,819 (0.28%) number of secondary alignments = 0 number of mapped bases = 134,235,739 bp number of sequenced bases = 134,197,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,950 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4289 >>>>>>> ACTG content number of A's = 34,883,249 bp (25.99%) number of C's = 25,592,313 bp (19.07%) number of T's = 40,454,250 bp (30.15%) number of G's = 33,265,881 bp (24.79%) number of N's = 1,913 bp (0%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 655,946 number of insertions = 11,680 mapped reads with insertion percentage = 0.5% number of deletions = 24,345 mapped reads with deletion percentage = 1.05% homopolymer indels = 37.65% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.3645X There is a 3.75% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 14829270 0.059495418468786886 0.7609783012550313 chr2 243199373 12614854 0.05187042155737795 0.4389686511746788 chr3 198022430 9188688 0.04640225857242536 0.24237514947060226 chr4 191154276 5826039 0.030478203898509703 0.20890673174081884 chr5 180915260 5626549 0.031100466594139158 0.2002763293542076 chr6 171115067 8947056 0.05228678080113191 0.29268842846641807 chr7 159138663 9868708 0.06201326449500207 0.5187623046941535 chr8 146364022 7632365 0.052146455773127084 0.29706827134462366 chr9 141213431 5581820 0.03952754324055762 0.2956719132996636 chr10 135534747 7305666 0.05390253172494578 0.3319667351420827 chr11 135006516 4537566 0.033609977758406864 0.2658071623870878 chr12 133851895 5478742 0.040931374187866375 0.23538784346253228 chr13 115169878 2796529 0.02428177444105654 0.1748377204125397 chr14 107349540 2929405 0.027288472777806036 0.21639625558209424 chr15 102531392 3000286 0.02926212100972939 0.20084960253662307 chr16 90354753 2905784 0.03215972490124565 0.2157830219930961 chr17 81195210 3587907 0.044188653493229466 0.24372717583245598 chr18 78077248 4513957 0.05781398698888567 0.4956890605947847 chr19 59128983 3585108 0.060631991590317055 0.5171872033710168 chr20 63025520 2129378 0.033785964796482444 0.20856488029628617 chr21 48129895 1272246 0.026433591845567084 0.19747716958538136 chr22 51304566 1852036 0.036098853267757885 0.2146705828318283 chrMT 16571 7250 0.4375113149478004 0.7386843951283157 chrX 155270560 7944916 0.05116820600118915 0.29393907617481707 chrY 59373566 273614 0.004608347088332205 0.10229108851115858