BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083775.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 = 2,218,144 number of mapped reads = 1,188,119 (53.56%) number of supplementary alignments = 6,503 (0.29%) number of secondary alignments = 0 number of mapped bases = 76,220,512 bp number of sequenced bases = 76,195,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,566 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9686 >>>>>>> ACTG content number of A's = 21,516,540 bp (28.24%) number of C's = 14,127,211 bp (18.54%) number of T's = 23,413,143 bp (30.73%) number of G's = 17,137,409 bp (22.49%) number of N's = 844 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 640,110 number of insertions = 5,651 mapped reads with insertion percentage = 0.47% number of deletions = 16,004 mapped reads with deletion percentage = 1.34% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2024X There is a 2.24% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% 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 5939610 0.023829870417855448 0.25563946906290647 chr2 243199373 6511494 0.026774304224871502 0.2594704253783243 chr3 198022430 5242365 0.026473591905725024 0.17483757438259184 chr4 191154276 5082495 0.026588445240952916 0.1790573951989804 chr5 180915260 4730871 0.02614965149982373 0.1744933403164825 chr6 171115067 4424818 0.025858728150455625 0.18778063764511227 chr7 159138663 4177871 0.026253023126127432 0.22551099606917785 chr8 146364022 3863403 0.026395851570681764 0.21393719431473887 chr9 141213431 3218143 0.02278921330082264 0.19287524154355518 chr10 135534747 3567016 0.026318092437210953 0.20501713572147284 chr11 135006516 3406744 0.02523392278340106 0.19440377879629347 chr12 133851895 3547497 0.026503151113400375 0.17691610000321742 chr13 115169878 2557881 0.02220963540484084 0.1614333552372591 chr14 107349540 2396770 0.02232678407378364 0.16497819716216355 chr15 102531392 2110705 0.02058593918241157 0.15723015525571027 chr16 90354753 2024407 0.02240509694050074 0.1708303265404677 chr17 81195210 1949433 0.024009211873459037 0.17988697794317546 chr18 78077248 2074582 0.02657089040843243 0.3218616511137098 chr19 59128983 1322437 0.02236529249961901 0.2167457713913468 chr20 63025520 1504811 0.023876217126014985 0.17148420102958803 chr21 48129895 1001122 0.020800419365136782 0.158772947966446 chr22 51304566 769517 0.014998996385623844 0.13137022563209447 chrMT 16571 88594 5.346327922273852 3.668118492106409 chrX 155270560 4532809 0.02919297128831119 0.19425499572463195 chrY 59373566 175117 0.0029494101802812383 0.07322016106265158