BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238491.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 = 3,623,196 number of mapped reads = 3,165,754 (87.37%) number of supplementary alignments = 25,920 (0.72%) number of secondary alignments = 0 number of mapped bases = 195,076,491 bp number of sequenced bases = 194,994,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,488,276 duplication rate = 20.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3439 >>>>>>> ACTG content number of A's = 48,531,330 bp (24.89%) number of C's = 33,543,165 bp (17.2%) number of T's = 66,795,124 bp (34.25%) number of G's = 46,120,228 bp (23.65%) number of N's = 4,564 bp (0%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,080,516 number of insertions = 13,415 mapped reads with insertion percentage = 0.42% number of deletions = 48,708 mapped reads with deletion percentage = 1.52% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.063X std coverageData = 1.3227X There is a 1.24% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 26194263 0.10509206715276348 1.830040542009236 chr2 243199373 16112590 0.06625259679431822 2.383085776149556 chr3 198022430 4797523 0.0242271696191184 0.5600816368862466 chr4 191154276 10638382 0.05565338229734395 0.8682808450968138 chr5 180915260 5960709 0.03294751918660704 0.6657584596568499 chr6 171115067 6097319 0.03563285867748864 1.0945232187188656 chr7 159138663 21636705 0.13596133455010867 1.5843626560607178 chr8 146364022 10261966 0.07011262644859541 1.3702701277767688 chr9 141213431 3533382 0.025021571779528535 0.5662579639428289 chr10 135534747 12914702 0.09528701890740977 1.2525064455078188 chr11 135006516 4220995 0.031265120566476956 0.6168273800145457 chr12 133851895 6772883 0.050599829012506696 0.8216269472654317 chr13 115169878 7880164 0.06842209210293684 1.1738113252877787 chr14 107349540 2034078 0.018948176210163547 0.5006775905022391 chr15 102531392 7795946 0.07603472310216954 1.1627377190114598 chr16 90354753 4051958 0.04484499005824298 0.8164193376583379 chr17 81195210 1536064 0.018918160320048436 0.44034471561627614 chr18 78077248 24890507 0.3187933442531171 3.414708467771586 chr19 59128983 2591013 0.04381967807564016 1.1356981987518675 chr20 63025520 6938173 0.11008513694135329 1.3203008815568735 chr21 48129895 1450687 0.030141079676155536 0.6218815443184601 chr22 51304566 653878 0.012745025462256128 0.3864715545868857 chrMT 16571 428207 25.840745881359002 27.634118050614784 chrX 155270560 5322651 0.03427984673978119 0.6733887299344179 chrY 59373566 361746 0.006092711359125709 0.38487184069530755