BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013335.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 = 2,882,101 number of mapped reads = 2,499,035 (86.71%) number of supplementary alignments = 36,402 (1.26%) number of secondary alignments = 0 number of mapped bases = 164,921,306 bp number of sequenced bases = 164,856,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 316,128 duplication rate = 9.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.8776 >>>>>>> ACTG content number of A's = 45,478,253 bp (27.59%) number of C's = 31,373,806 bp (19.03%) number of T's = 51,245,748 bp (31.09%) number of G's = 36,740,185 bp (22.29%) number of N's = 18,719 bp (0.01%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,169,835 number of insertions = 11,248 mapped reads with insertion percentage = 0.45% number of deletions = 36,273 mapped reads with deletion percentage = 1.44% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.0533X std coverageData = 0.5118X There is a 2.87% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 2390282 0.009589873800153942 0.2265218819268473 chr2 243199373 33238954 0.13667368295394414 0.8271853640350767 chr3 198022430 1581227 0.007985090375873076 0.14262043373367891 chr4 191154276 3922853 0.020521921256943267 0.40233912257311516 chr5 180915260 16380320 0.09054139490499585 0.5236137046659889 chr6 171115067 1998966 0.011681998757011853 0.1839240282833346 chr7 159138663 11943279 0.07504951200953598 0.4656359836124042 chr8 146364022 6522606 0.044564271402708515 0.37401988957734816 chr9 141213431 21641018 0.15325042275900796 0.9083510999577531 chr10 135534747 4483645 0.033081147818131096 0.6390346898903051 chr11 135006516 1131021 0.008377528977934664 0.21594126867329055 chr12 133851895 1497083 0.01118462312393859 0.29626153112255244 chr13 115169878 5158542 0.04479072210183291 0.3559440782982638 chr14 107349540 1927662 0.017956872474721365 0.4805285304075718 chr15 102531392 3543673 0.03456183448674919 0.3170137882076224 chr16 90354753 1110008 0.012284998443856075 0.36783244444417007 chr17 81195210 1554041 0.019139565006359365 0.25192627700105014 chr18 78077248 8425274 0.10790946422701783 1.050779688960546 chr19 59128983 670458 0.01133890633633932 0.2865754390817801 chr20 63025520 538663 0.008546744239476326 0.2006759339558006 chr21 48129895 693645 0.014411936697555645 0.42216213529010477 chr22 51304566 381797 0.00744177428574291 0.13547412946719942 chrMT 16571 66117 3.9899221531591333 3.6762505839369037 chrX 155270560 33379474 0.214976193812916 0.8292755127892265 chrY 59373566 740698 0.01247521498035001 0.3748091964265244