BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004050.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 = 2,434,743 number of mapped reads = 2,073,839 (85.18%) number of supplementary alignments = 24,676 (1.01%) number of secondary alignments = 0 number of mapped bases = 135,569,607 bp number of sequenced bases = 135,513,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,879 duplication rate = 10.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0985 >>>>>>> ACTG content number of A's = 37,392,322 bp (27.59%) number of C's = 25,481,741 bp (18.8%) number of T's = 42,319,719 bp (31.23%) number of G's = 30,303,585 bp (22.36%) number of N's = 15,945 bp (0.01%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,081,347 number of insertions = 10,703 mapped reads with insertion percentage = 0.51% number of deletions = 31,669 mapped reads with deletion percentage = 1.51% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.575X There is a 2.17% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% 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 0.01% 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 14097228 0.056558446849366124 1.077639121559073 chr2 243199373 3722067 0.015304591266359885 0.6108444873708246 chr3 198022430 5717310 0.028872032324823 0.2976961591897509 chr4 191154276 5543973 0.02900261043598104 0.37054096553731375 chr5 180915260 6863409 0.037937148032730905 0.34462038704486675 chr6 171115067 6121109 0.03577188793082727 0.5041830627641365 chr7 159138663 2037630 0.012804116621238674 0.28779326090279217 chr8 146364022 13601202 0.09292722223771631 0.618804174618722 chr9 141213431 10467967 0.07412869247543458 0.6599669420565822 chr10 135534747 6583453 0.04857391293171485 0.5832702709464889 chr11 135006516 2710641 0.020077853131177756 0.3620425597165135 chr12 133851895 3515126 0.02626130918803951 0.30507469688834127 chr13 115169878 6112060 0.053069952891675376 0.4054991090451627 chr14 107349540 4631329 0.04314251369870798 0.40900097851626055 chr15 102531392 2306932 0.022499762804351665 0.27826546558024384 chr16 90354753 7897391 0.08740426748773249 0.5932995468005727 chr17 81195210 1161826 0.014309046063185255 0.21980953406956988 chr18 78077248 7458930 0.09553269602945022 1.129132252997324 chr19 59128983 2036866 0.03444784429997722 0.8747641917000615 chr20 63025520 1228493 0.019491993084706005 0.2552158677406507 chr21 48129895 1387913 0.028836817533053002 0.36136951720706256 chr22 51304566 796048 0.01551612384753435 0.21173851781291886 chrMT 16571 18993 1.1461589523866997 1.663468980419953 chrX 155270560 18882952 0.12161321502286074 0.727040025326844 chrY 59373566 668759 0.011263581506962207 0.28184795737031265