BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716650.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,562,620 number of mapped reads = 1,432,433 (91.67%) number of supplementary alignments = 43,319 (2.77%) number of secondary alignments = 0 number of mapped bases = 107,145,582 bp number of sequenced bases = 107,106,072 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,735 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6961 >>>>>>> ACTG content number of A's = 26,841,064 bp (25.06%) number of C's = 22,733,552 bp (21.23%) number of T's = 31,214,759 bp (29.14%) number of G's = 26,304,071 bp (24.56%) number of N's = 12,626 bp (0.01%) GC percentage = 45.78% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 804,217 number of insertions = 8,166 mapped reads with insertion percentage = 0.56% number of deletions = 22,335 mapped reads with deletion percentage = 1.54% homopolymer indels = 40.07% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.2792X There is a 3.1% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 9442658 0.037884190467072094 0.3820996479895397 chr2 243199373 9428754 0.03876964765036627 0.40353288050343666 chr3 198022430 7341095 0.03707203774845102 0.20955845747211488 chr4 191154276 4122971 0.02156881387262297 0.17299042835288964 chr5 180915260 6048354 0.0334319725157513 0.19850912901316686 chr6 171115067 6815878 0.03983213237440979 0.2275094549905218 chr7 159138663 5846157 0.03673624554706734 0.3682379912004272 chr8 146364022 7449745 0.05089874477486004 0.35120000494822773 chr9 141213431 5046353 0.035735644720649835 0.26884409501867285 chr10 135534747 6335936 0.04674768751366762 0.35608564529665826 chr11 135006516 4251941 0.031494339132490466 0.24244381521826905 chr12 133851895 4448847 0.033237086408078126 0.19882687379785374 chr13 115169878 3907419 0.03392743890898278 0.2004410219618897 chr14 107349540 2593975 0.024163820357311266 0.17994994010637003 chr15 102531392 2840227 0.0277010478898014 0.18187591287029073 chr16 90354753 2731404 0.030229776622819168 0.20403596198036905 chr17 81195210 3414824 0.04205696370512497 0.24714190165154606 chr18 78077248 2408724 0.03085052382993827 0.38907955111993453 chr19 59128983 1941978 0.03284308137009561 0.32228812671592943 chr20 63025520 1974469 0.03132808741601815 0.19555885248959393 chr21 48129895 1751562 0.036392391880347964 0.21951313158879407 chr22 51304566 1345173 0.026219362229864686 0.1779643827603756 chrMT 16571 3643 0.2198418924627361 0.5023699782641735 chrX 155270560 5335283 0.034361201505295015 0.22715032701237337 chrY 59373566 318212 0.005359489440132331 0.17962560770938477