BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084255.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 = 3,476,137 number of mapped reads = 2,209,355 (63.56%) number of supplementary alignments = 14,259 (0.41%) number of secondary alignments = 0 number of mapped bases = 140,657,834 bp number of sequenced bases = 140,611,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,213 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5565 >>>>>>> ACTG content number of A's = 39,157,348 bp (27.85%) number of C's = 27,419,044 bp (19.5%) number of T's = 42,302,057 bp (30.08%) number of G's = 31,731,958 bp (22.57%) number of N's = 1,524 bp (0%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,135,799 number of insertions = 10,202 mapped reads with insertion percentage = 0.46% number of deletions = 28,748 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0454X std coverageData = 0.3085X There is a 3.86% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% 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 11120258 0.044614765473342595 0.42830156754957754 chr2 243199373 11464036 0.0471384274498109 0.39675585849732775 chr3 198022430 9259683 0.04676077856432728 0.24643752243792144 chr4 191154276 9331501 0.04881659565909998 0.25986592590171775 chr5 180915260 8828274 0.04879784049173077 0.25270541033996524 chr6 171115067 8160982 0.047692948044136874 0.28289906156675737 chr7 159138663 7808683 0.049068421543795426 0.3746389936119535 chr8 146364022 7032422 0.04804747713205094 0.3086464596913001 chr9 141213431 6032422 0.042718472012764845 0.28788688369948007 chr10 135534747 6453072 0.0476119382138958 0.30804875551110456 chr11 135006516 6774683 0.050180414995673245 0.28640772664264014 chr12 133851895 6633958 0.04956192812959428 0.25730528075613973 chr13 115169878 4476408 0.038867871336982746 0.22830574014711924 chr14 107349540 4290029 0.03996318009373864 0.24148589851182664 chr15 102531392 4346438 0.042391290269423045 0.24392126422006835 chr16 90354753 3680998 0.040739395303310715 0.2485022199494889 chr17 81195210 3674680 0.04525734954069335 0.2563393775369605 chr18 78077248 3771272 0.04830180489968089 0.508098781086488 chr19 59128983 2807526 0.04748138489038447 0.3692632992302382 chr20 63025520 2760911 0.04380623912345348 0.245758893453347 chr21 48129895 1777988 0.03694144772183692 0.22513135387682234 chr22 51304566 1604960 0.031282985611845934 0.20217260616314142 chrMT 16571 36036 2.174642447649508 2.01041254676147 chrX 155270560 8198606 0.052802063700935965 0.28703745680073994 chrY 59373566 332008 0.00559184873618674 0.11405553077316918