BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240268.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 = 2,001,687 number of mapped reads = 1,559,414 (77.9%) number of supplementary alignments = 4,839 (0.24%) number of secondary alignments = 0 number of mapped bases = 92,354,280 bp number of sequenced bases = 92,297,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,796 duplication rate = 6.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9341 >>>>>>> ACTG content number of A's = 23,829,129 bp (25.82%) number of C's = 15,910,873 bp (17.24%) number of T's = 29,007,999 bp (31.43%) number of G's = 23,528,095 bp (25.49%) number of N's = 21,670 bp (0.02%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 931,821 number of insertions = 7,439 mapped reads with insertion percentage = 0.47% number of deletions = 32,386 mapped reads with deletion percentage = 2.05% homopolymer indels = 49.17% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.2977X There is a 2.28% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 6704805 0.026899852738982745 0.2908617602230992 chr2 243199373 9120057 0.037500331055541 0.49622155668176593 chr3 198022430 6939764 0.035045343095729105 0.25038918266596155 chr4 191154276 6444525 0.0337137370654476 0.24550222712759434 chr5 180915260 5035372 0.027832765461575766 0.21878743704858436 chr6 171115067 5449095 0.03184462417912036 0.26983945365940004 chr7 159138663 5633865 0.035402239115204834 0.5527383820086014 chr8 146364022 5334860 0.036449258001396 0.29881738475569836 chr9 141213431 3504563 0.02481749062523663 0.23431454619399072 chr10 135534747 3870374 0.028556322903675765 0.24230085912596816 chr11 135006516 4065714 0.03011494645191792 0.25037809776618253 chr12 133851895 4283006 0.03199809759884236 0.23468470853862763 chr13 115169878 2139457 0.018576532658999605 0.184682670119497 chr14 107349540 3197874 0.029789359134654886 0.23787700984668447 chr15 102531392 2053964 0.020032537937259256 0.22860990885246962 chr16 90354753 2590702 0.02867255915137082 0.22362649458138065 chr17 81195210 2917791 0.03593550654034887 0.2571165984575798 chr18 78077248 2310654 0.029594460091626182 0.3258537552136026 chr19 59128983 1885264 0.0318839239971369 0.2713915023881917 chr20 63025520 1984541 0.03148789569685423 0.2344089570533313 chr21 48129895 1382799 0.02873056340555075 0.22779793714523308 chr22 51304566 1037243 0.02021736232989477 0.18464353753582616 chrMT 16571 64630 3.900187073803633 4.141674569077204 chrX 155270560 4213206 0.027134609419841083 0.2328623849808838 chrY 59373566 190155 0.003202687876284877 0.08029744043053837