BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525190.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 = 1,906,689 number of mapped reads = 1,759,630 (92.29%) number of supplementary alignments = 5,609 (0.29%) number of secondary alignments = 0 number of mapped bases = 101,717,829 bp number of sequenced bases = 101,685,734 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,267 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7124 >>>>>>> ACTG content number of A's = 24,145,755 bp (23.75%) number of C's = 19,387,282 bp (19.07%) number of T's = 32,281,060 bp (31.75%) number of G's = 25,869,238 bp (25.44%) number of N's = 2,399 bp (0%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 513,916 number of insertions = 5,773 mapped reads with insertion percentage = 0.33% number of deletions = 20,261 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.44% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.3122X There is a 2.93% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 10425739 0.04182833710973984 0.5106198756980919 chr2 243199373 8157396 0.0335420108176019 0.4373315942294511 chr3 198022430 8060883 0.04070691890812571 0.22361416548744817 chr4 191154276 5471061 0.02862118030778448 0.19765454692245704 chr5 180915260 4385759 0.02424206227821799 0.17164669010735373 chr6 171115067 6080711 0.03553580118108477 0.23248964990336082 chr7 159138663 6476362 0.04069634542549851 0.5321325410888855 chr8 146364022 5504054 0.03760523880656955 0.3077779122093861 chr9 141213431 3174393 0.022479398577887395 0.21195678993218472 chr10 135534747 6395701 0.04718864454736467 0.32796172389916406 chr11 135006516 4546743 0.03367795225528226 0.2587982158365526 chr12 133851895 4430279 0.03309836592152842 0.20215847814432242 chr13 115169878 2993139 0.0259889048419414 0.17852609670092573 chr14 107349540 3678379 0.03426543793294317 0.20585865347977958 chr15 102531392 2902128 0.02830477518534031 0.18761485069402098 chr16 90354753 2990888 0.03310161226382856 0.2177114819895238 chr17 81195210 1980637 0.02439352025815316 0.17773417704644145 chr18 78077248 2078789 0.026624772942816836 0.3963845625783587 chr19 59128983 1552868 0.026262383034729348 0.37371972753954263 chr20 63025520 1809723 0.02871413040304943 0.19005622052862134 chr21 48129895 1260305 0.026185492405499743 0.19288880560707952 chr22 51304566 862932 0.016819789490081644 0.14239094200230185 chrMT 16571 344447 20.786132399975862 11.385691870975275 chrX 155270560 5837085 0.037592992515773756 0.2343642874246692 chrY 59373566 317428 0.00534628491069578 0.16513891751708426