BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238524.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 = 2,441,791 number of mapped reads = 2,163,074 (88.59%) number of supplementary alignments = 18,125 (0.74%) number of secondary alignments = 0 number of mapped bases = 134,141,721 bp number of sequenced bases = 134,082,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 458,153 duplication rate = 16.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3877 >>>>>>> ACTG content number of A's = 33,536,233 bp (25.01%) number of C's = 23,917,414 bp (17.84%) number of T's = 44,235,813 bp (32.99%) number of G's = 32,383,947 bp (24.15%) number of N's = 9,305 bp (0.01%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 752,762 number of insertions = 8,092 mapped reads with insertion percentage = 0.37% number of deletions = 33,716 mapped reads with deletion percentage = 1.54% homopolymer indels = 43.49% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.5112X There is a 2.55% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 7524859 0.030189930800613732 0.7460137960368352 chr2 243199373 9342390 0.03841453160325376 0.9715190939267386 chr3 198022430 12585571 0.06355629006269643 0.39588637095510815 chr4 191154276 6469396 0.033843846632026164 0.2920148527796714 chr5 180915260 10372864 0.05733548402716277 0.37321599096833574 chr6 171115067 7238912 0.042304351842961906 0.4441598790268228 chr7 159138663 5332570 0.033508953132275594 0.4051207854562668 chr8 146364022 16874674 0.11529249995603427 0.7324903080456505 chr9 141213431 4359712 0.03087321063674177 0.3958474358724538 chr10 135534747 4003214 0.029536440570475997 0.35583510294815585 chr11 135006516 3519558 0.026069541710120124 0.3066376490063059 chr12 133851895 2498873 0.01866894002509266 0.22909565194831902 chr13 115169878 2477943 0.02151554766776778 0.2860966767418037 chr14 107349540 2009352 0.018717844529189412 0.21889056684136554 chr15 102531392 7336389 0.07155261288172114 0.44594359464161587 chr16 90354753 5416515 0.0599472060977246 0.40515715392884705 chr17 81195210 2455194 0.03023816306405267 0.2813510109366646 chr18 78077248 7725069 0.09894135869133093 0.8557904321614561 chr19 59128983 2676854 0.04527143651362987 0.5330177008329166 chr20 63025520 6360787 0.10092399078976262 0.5091478184608713 chr21 48129895 982132 0.02040586209465032 0.23408067688564807 chr22 51304566 1296847 0.02527741877789201 0.25224052814512826 chrMT 16571 19659 1.1863496469736285 1.9344401089031544 chrX 155270560 4945983 0.031853965104524644 0.2996730087588838 chrY 59373566 316404 0.005329038178370489 0.20017778248688672