BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080664.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,455,949 number of mapped reads = 1,335,163 (91.7%) number of supplementary alignments = 12,338 (0.85%) number of secondary alignments = 0 number of mapped bases = 89,457,477 bp number of sequenced bases = 89,423,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,947 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6774 >>>>>>> ACTG content number of A's = 24,417,728 bp (27.31%) number of C's = 16,872,126 bp (18.87%) number of T's = 27,883,688 bp (31.18%) number of G's = 20,245,906 bp (22.64%) number of N's = 4,064 bp (0%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 596,404 number of insertions = 6,763 mapped reads with insertion percentage = 0.5% number of deletions = 20,742 mapped reads with deletion percentage = 1.54% homopolymer indels = 48% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2305X There is a 2.53% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 10531488 0.04225260485910685 0.2784378072249496 chr2 243199373 5989450 0.024627736190750787 0.31478971689409124 chr3 198022430 5700051 0.028784875531524385 0.1880594617293153 chr4 191154276 3752067 0.019628475378704057 0.1593254521970753 chr5 180915260 4045124 0.02235921944892874 0.16471344779615013 chr6 171115067 5344737 0.031234753863024815 0.2275410243303032 chr7 159138663 5435328 0.0341546667386542 0.39501467638588356 chr8 146364022 10675296 0.07293661279682516 0.32845168616891696 chr9 141213431 2760542 0.019548721254425156 0.18092268570307488 chr10 135534747 4261871 0.03144485893348072 0.21005768689091434 chr11 135006516 3747967 0.027761378569312906 0.22221179005748454 chr12 133851895 2903782 0.021693992453375426 0.16482955564696616 chr13 115169878 1848917 0.01605382442100008 0.14041104286959694 chr14 107349540 1794488 0.016716308239420496 0.14850676397948065 chr15 102531392 1640730 0.016002221056357062 0.14683145896672045 chr16 90354753 2330511 0.025792898797476652 0.18144476251067934 chr17 81195210 1471922 0.018128187611067204 0.15137496107488319 chr18 78077248 2900548 0.03714972126066739 0.26020733021737047 chr19 59128983 1544778 0.02612556349903735 0.20039087068698977 chr20 63025520 2383838 0.03782337694318111 0.21879213779059606 chr21 48129895 1347059 0.02798798958526712 0.1912904383940975 chr22 51304566 950896 0.018534334741278195 0.15050917261748953 chrMT 16571 17774 1.0725967050872005 1.1967411787299367 chrX 155270560 5898213 0.037986679509625004 0.22430046185409563 chrY 59373566 180100 0.003033336417758704 0.06650945773629771