BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237338.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 = 3,346,975 number of mapped reads = 3,081,990 (92.08%) number of supplementary alignments = 21,034 (0.63%) number of secondary alignments = 0 number of mapped bases = 191,967,279 bp number of sequenced bases = 191,853,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 351,569 duplication rate = 9.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5587 >>>>>>> ACTG content number of A's = 50,722,757 bp (26.44%) number of C's = 32,533,982 bp (16.96%) number of T's = 64,583,207 bp (33.66%) number of G's = 43,992,470 bp (22.93%) number of N's = 20,835 bp (0.01%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,181,779 number of insertions = 13,208 mapped reads with insertion percentage = 0.43% number of deletions = 64,897 mapped reads with deletion percentage = 2.08% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.062X std coverageData = 0.639X There is a 4.64% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 17249097 0.06920382758043359 0.6784862505947034 chr2 243199373 7504684 0.030858155214076147 1.0656141068059004 chr3 198022430 12530815 0.06327977593245371 0.32246411277528864 chr4 191154276 12563486 0.0657243262504889 0.39240950359853727 chr5 180915260 10531687 0.05821337017120612 0.31280527151611776 chr6 171115067 24318934 0.14212035460325653 0.770904751738113 chr7 159138663 11465452 0.07204692928707086 0.8754600467470636 chr8 146364022 15971969 0.10912496651670313 1.3516856718361518 chr9 141213431 8692608 0.06155652432239254 0.42981535669026855 chr10 135534747 9149923 0.06750979510811349 0.6109536242572051 chr11 135006516 7738347 0.05731832232453136 0.38580883294038787 chr12 133851895 4282249 0.03199244209430132 0.2540965845854104 chr13 115169878 10712343 0.09301340928745275 0.4364511435966592 chr14 107349540 5623994 0.05238954913081137 0.3184178365377007 chr15 102531392 3972685 0.03874603594575211 0.29169109063533094 chr16 90354753 3997233 0.04423932186500471 0.32898267301727885 chr17 81195210 3310979 0.04077800894905007 0.3711824487099778 chr18 78077248 4495181 0.05757350720148333 1.0694803982895333 chr19 59128983 1211689 0.02049230239593331 0.5001710797545504 chr20 63025520 2005702 0.03182364857917872 0.24326395426447703 chr21 48129895 3447923 0.07163786665231661 0.3833179858913364 chr22 51304566 533227 0.010393363428900265 0.12467317983696027 chrMT 16571 4231 0.2553255687647094 0.6142752324247851 chrX 155270560 10086278 0.06495937156406212 0.3850265741084947 chrY 59373566 566563 0.009542344146888532 0.2948419443213718