BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004042.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 = 1,913,310 number of mapped reads = 1,758,224 (91.89%) number of supplementary alignments = 14,496 (0.76%) number of secondary alignments = 0 number of mapped bases = 117,136,151 bp number of sequenced bases = 117,083,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,935 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0923 >>>>>>> ACTG content number of A's = 33,619,114 bp (28.71%) number of C's = 21,578,154 bp (18.43%) number of T's = 36,291,338 bp (31%) number of G's = 25,569,891 bp (21.84%) number of N's = 25,480 bp (0.02%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 909,179 number of insertions = 8,794 mapped reads with insertion percentage = 0.5% number of deletions = 30,149 mapped reads with deletion percentage = 1.69% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3921X There is a 3.39% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 8665170 0.034764888308944274 0.6826401842231571 chr2 243199373 9252154 0.03804349446246311 0.415439019996092 chr3 198022430 7835377 0.03956812872157967 0.2144532369596561 chr4 191154276 8675421 0.045384394121531446 0.2497247046822613 chr5 180915260 6696437 0.0370142187010648 0.21281858980801724 chr6 171115067 7342173 0.04290781126830871 0.2441304913441367 chr7 159138663 6992783 0.04394144620908371 0.5772442615239498 chr8 146364022 6516011 0.04451921251521771 0.6507419786188655 chr9 141213431 5008721 0.03546915448856986 0.39241941082599424 chr10 135534747 4952879 0.036543241564467595 0.2959570075543382 chr11 135006516 5068813 0.03754495079333801 0.3918464199713522 chr12 133851895 5116488 0.03822499487213087 0.22031698099781255 chr13 115169878 3898611 0.033850960578424856 0.19798029001316889 chr14 107349540 3523416 0.032821901239632696 0.23004176993494843 chr15 102531392 3210807 0.0313153555937288 0.21122120310937562 chr16 90354753 2865124 0.031709720904222936 0.22969236868122442 chr17 81195210 2633396 0.032432898443147076 0.23688069571581885 chr18 78077248 3841596 0.04920250262919103 0.7547111420918653 chr19 59128983 1858053 0.03142372666886559 0.46991618675323077 chr20 63025520 2312211 0.036686900798279805 0.22840230111023457 chr21 48129895 1465187 0.030442347734188906 0.22187703126121375 chr22 51304566 1124733 0.021922668637329473 0.1580894835374811 chrMT 16571 9272 0.5595317120270352 0.9251400430926099 chrX 155270560 7936021 0.05111091890181886 0.2892056494152117 chrY 59373566 335297 0.005647243758274516 0.11305673637403411