BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238239.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 = 2,177,587 number of mapped reads = 1,837,305 (84.37%) number of supplementary alignments = 27,379 (1.26%) number of secondary alignments = 0 number of mapped bases = 120,048,396 bp number of sequenced bases = 119,991,662 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 260,817 duplication rate = 9.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4445 >>>>>>> ACTG content number of A's = 34,431,583 bp (28.69%) number of C's = 23,750,665 bp (19.79%) number of T's = 36,073,681 bp (30.06%) number of G's = 25,715,143 bp (21.43%) number of N's = 20,590 bp (0.02%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,031,098 number of insertions = 9,956 mapped reads with insertion percentage = 0.54% number of deletions = 34,150 mapped reads with deletion percentage = 1.84% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.4331X There is a 1.84% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% 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 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 5972671 0.02396251201315964 0.3666197820916937 chr2 243199373 11845461 0.04870679086824784 0.538255139337831 chr3 198022430 6571364 0.03318494778596546 0.3436592799276731 chr4 191154276 8273163 0.04328003104675514 0.39460024325313675 chr5 180915260 4898166 0.02707436619774363 0.3085878143877896 chr6 171115067 5272418 0.03081212012732929 0.35359751811386747 chr7 159138663 7981397 0.05015372662770203 0.6011843362711518 chr8 146364022 7020404 0.04796536678938763 0.5377611681537174 chr9 141213431 4403491 0.031183230722579072 0.39165103476911606 chr10 135534747 10212341 0.07534850823161975 0.5892979023569104 chr11 135006516 5125273 0.037963152830341906 0.41708125729756923 chr12 133851895 8204327 0.0612940668490349 0.471469975123829 chr13 115169878 1540612 0.013376865780825087 0.22558364129696765 chr14 107349540 7764749 0.07233146038632303 0.5670679720515241 chr15 102531392 4707132 0.045909178722551625 0.4746773376820312 chr16 90354753 3077162 0.03405644858549942 0.35377114056507103 chr17 81195210 2004226 0.024684042322201026 0.29494105831314044 chr18 78077248 1825798 0.02338450760969444 0.5998077588267661 chr19 59128983 800542 0.013538910351290838 0.30258649399983645 chr20 63025520 4462118 0.07079859079306287 0.5141902131934888 chr21 48129895 1521129 0.0316046606791891 0.32808900342767217 chr22 51304566 1400038 0.027288760224577283 0.3067660005245368 chrMT 16571 7579 0.4573652766881902 1.1161129326591956 chrX 155270560 4859485 0.03129688590032779 0.35178154929510164 chrY 59373566 297350 0.005008120954028599 0.1250877551736693