BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240022.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 = 1,430,403 number of mapped reads = 1,013,996 (70.89%) number of supplementary alignments = 8,277 (0.58%) number of secondary alignments = 0 number of mapped bases = 64,041,153 bp number of sequenced bases = 64,015,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,324 duplication rate = 10.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8574 >>>>>>> ACTG content number of A's = 17,677,926 bp (27.62%) number of C's = 11,465,380 bp (17.91%) number of T's = 20,530,205 bp (32.07%) number of G's = 14,299,608 bp (22.34%) number of N's = 42,144 bp (0.07%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 565,003 number of insertions = 4,489 mapped reads with insertion percentage = 0.44% number of deletions = 15,348 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2732X There is a 1.23% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.08% 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% 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 5050912 0.020264390835760444 0.34865273913301914 chr2 243199373 5586226 0.022969738495172847 0.2926414454424992 chr3 198022430 4250786 0.02146618441153358 0.22587422326491124 chr4 191154276 3865452 0.020221635010665418 0.22464267934269957 chr5 180915260 3671135 0.02029201406227424 0.22177512830084994 chr6 171115067 4256134 0.02487293535641721 0.2563133493997556 chr7 159138663 3761440 0.023636242312781025 0.3603364057983713 chr8 146364022 3185313 0.021762950733890053 0.41736021996905304 chr9 141213431 2520926 0.01785188549097713 0.2528968660089492 chr10 135534747 2898816 0.02138799137611553 0.2588180323288077 chr11 135006516 2936229 0.02174879470262013 0.24441987655905215 chr12 133851895 2790761 0.020849618901547864 0.22785555411188377 chr13 115169878 2521755 0.021895959636251416 0.2310795057754402 chr14 107349540 2217840 0.020659986060489872 0.23097102505880446 chr15 102531392 1992819 0.01943618399328861 0.22923963288321988 chr16 90354753 1701988 0.018836729042909343 0.21399305872422364 chr17 81195210 1653769 0.02036781480089774 0.22307700147477164 chr18 78077248 1468208 0.01880455622616207 0.4219732246976358 chr19 59128983 984188 0.01664476454803899 0.2738752794105331 chr20 63025520 1341154 0.02127953882808107 0.23230865984106927 chr21 48129895 809529 0.01681967101735834 0.2025418466454496 chr22 51304566 586969 0.011440872533645445 0.15939765259001784 chrMT 16571 26506 1.599541367449158 2.1044929334417875 chrX 155270560 3789395 0.02440510937810748 0.25072705689108676 chrY 59373566 172903 0.002912120858632611 0.0871738105398126