BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472528.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,163,478 number of mapped reads = 18,956,854 (98.92%) number of supplementary alignments = 75,658 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,504,625 number of mapped paired reads (second in pair) = 9,452,229 number of mapped paired reads (both in pair) = 18,848,676 number of mapped paired reads (singletons) = 108,178 number of mapped bases = 1,869,200,206 bp number of sequenced bases = 1,868,974,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,305,081 duplication rate = 45.88% >>>>>>> Insert size mean insert size = 29,493.9896 std insert size = 1,642,929.5907 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 54.824 >>>>>>> ACTG content number of A's = 506,388,570 bp (27.09%) number of C's = 430,326,450 bp (23.02%) number of T's = 504,083,192 bp (26.97%) number of G's = 427,886,078 bp (22.89%) number of N's = 290,270 bp (0.02%) GC percentage = 45.92% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 10,920,136 number of insertions = 103,838 mapped reads with insertion percentage = 0.54% number of deletions = 94,340 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.6038X std coverageData = 22.6275X There is a 5.79% of reference with a coverageData >= 1X There is a 2.51% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 197664145 0.7930337112379752 31.589802886389794 chr2 243199373 87879533 0.36134769557979085 13.322519151443212 chr3 198022430 234347604 1.1834396941800986 31.285805555930406 chr4 191154276 60558452 0.3168040666796279 13.70322156126403 chr5 180915260 96634916 0.5341446376607479 17.38281064446437 chr6 171115067 130728225 0.7639784578408867 22.528334301443728 chr7 159138663 102661975 0.6451102017867273 22.828694887268185 chr8 146364022 82469997 0.5634581222426369 17.935398805253254 chr9 141213431 113308083 0.8023888535078508 32.35783099385119 chr10 135534747 61507197 0.4538112798484067 23.22587137006748 chr11 135006516 68516189 0.5075028304559759 16.983195505614933 chr12 133851895 110128850 0.8227664613937666 22.662267958729934 chr13 115169878 53264383 0.46248536444572774 18.850085694276284 chr14 107349540 58161953 0.5417997412937214 34.28437358640665 chr15 102531392 43856914 0.42774133018695387 12.716375809207152 chr16 90354753 64201142 0.7105452659474372 24.267226679947168 chr17 81195210 77967799 0.9602512143265595 25.24230647686948 chr18 78077248 34614403 0.4433353363069354 19.117594106615964 chr19 59128983 36352079 0.6147929011395309 17.216712821289104 chr20 63025520 28020395 0.4445880811455423 12.522376201007086 chr21 48129895 7005510 0.14555423401609333 4.767814681487435 chr22 51304566 10619870 0.2069965858399426 5.8996002080176915 chrMT 16571 2637 0.15913342586446202 0.5032032861006875 chrX 155270560 104602293 0.6736775664362903 27.182277196031382 chrY 59373566 4125662 0.06948651189318829 3.7803786381442546