BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238515.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 = 3,434,339 number of mapped reads = 2,043,871 (59.51%) number of supplementary alignments = 16,804 (0.49%) number of secondary alignments = 0 number of mapped bases = 122,984,459 bp number of sequenced bases = 122,918,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 933,491 duplication rate = 23.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9535 >>>>>>> ACTG content number of A's = 29,645,733 bp (24.12%) number of C's = 21,043,944 bp (17.12%) number of T's = 42,135,265 bp (34.28%) number of G's = 30,086,096 bp (24.48%) number of N's = 7,749 bp (0.01%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 748,005 number of insertions = 7,576 mapped reads with insertion percentage = 0.37% number of deletions = 39,169 mapped reads with deletion percentage = 1.89% homopolymer indels = 40.96% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.7594X There is a 1.04% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 5819595 0.023348367103968017 0.5772100637223156 chr2 243199373 7655823 0.031479616520228446 1.449127722177178 chr3 198022430 4033851 0.020370677200557533 0.41902379915074334 chr4 191154276 22350664 0.11692473988915633 1.037928937577087 chr5 180915260 4863739 0.026884072686847976 0.49522884628123415 chr6 171115067 4622429 0.0270135709323598 0.6658512749731499 chr7 159138663 4628163 0.029082580642266674 0.5689977566750614 chr8 146364022 11205155 0.07655675791691485 0.8768509325092698 chr9 141213431 3772107 0.026712097944847753 0.5066769771426016 chr10 135534747 3861005 0.028487196718639245 0.5168881439187069 chr11 135006516 3434853 0.025442127548865864 0.4804667012286963 chr12 133851895 14082007 0.10520588445908816 1.035550714221488 chr13 115169878 3926254 0.03409097993487498 0.647320261371517 chr14 107349540 2651649 0.024701074638978426 0.5178544741370313 chr15 102531392 1714493 0.016721639749121907 0.44805110189568675 chr16 90354753 2155708 0.023858268972302983 0.4757555917404424 chr17 81195210 3575055 0.0440303682938932 0.6507128599954455 chr18 78077248 8275385 0.10598971162508186 1.4801657985400232 chr19 59128983 1838698 0.031096391426180963 0.5474254631098961 chr20 63025520 1794084 0.028465992823224623 0.5106694115363479 chr21 48129895 2177828 0.04524896636487572 0.6366586073371204 chr22 51304566 806944 0.015728502605401633 0.36063610953110287 chrMT 16571 9095 0.548850401303482 1.7782352189143875 chrX 155270560 3353000 0.021594563708664413 0.4239449434545508 chrY 59373566 376875 0.006347521723724662 0.27750077685420826