BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236112.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 = 1,667,044 number of mapped reads = 1,491,065 (89.44%) number of supplementary alignments = 9,299 (0.56%) number of secondary alignments = 0 number of mapped bases = 100,765,076 bp number of sequenced bases = 100,707,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,880 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5061 >>>>>>> ACTG content number of A's = 28,433,230 bp (28.23%) number of C's = 18,149,180 bp (18.02%) number of T's = 32,374,791 bp (32.15%) number of G's = 21,687,114 bp (21.53%) number of N's = 63,278 bp (0.06%) GC percentage = 39.56% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 860,874 number of insertions = 7,840 mapped reads with insertion percentage = 0.52% number of deletions = 32,579 mapped reads with deletion percentage = 2.16% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.3658X There is a 2.79% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 8334029 0.03343634197003666 0.6290249318775188 chr2 243199373 6039624 0.024834044288428326 0.3285669590025419 chr3 198022430 6994768 0.03532310960935082 0.21056620705207738 chr4 191154276 5664207 0.02963159976604447 0.21798625833169444 chr5 180915260 4167591 0.023036149631601006 0.1762702297116431 chr6 171115067 10581376 0.06183778077239686 0.3826257263669338 chr7 159138663 6999791 0.04398548327630476 0.5266234989791021 chr8 146364022 7607570 0.05197704938717795 0.7314527191462888 chr9 141213431 5277380 0.03737165765769122 0.3478544110932504 chr10 135534747 3398247 0.02507288407746834 0.28954232216894366 chr11 135006516 3653855 0.027064286289707674 0.2582704522989898 chr12 133851895 3475333 0.02596401791696711 0.18981910286524342 chr13 115169878 3284522 0.02851893270217756 0.18881396664008 chr14 107349540 2506790 0.023351660379727756 0.1894524911325924 chr15 102531392 2334003 0.022763789259781043 0.16958609052486612 chr16 90354753 2995056 0.033147741547143623 0.23789417368307667 chr17 81195210 2591522 0.03191717836557107 0.2282219101817332 chr18 78077248 3022662 0.0387137364267757 0.5982254723608729 chr19 59128983 2100331 0.035521175799692 0.45172152116920344 chr20 63025520 1852556 0.029393743994496197 0.19805872638432914 chr21 48129895 1859020 0.03862505829277209 0.24808682814257174 chr22 51304566 965723 0.018823334359752697 0.15141952651054588 chrMT 16571 90357 5.452718604791503 3.899831659586919 chrX 155270560 4728320 0.030452134648062068 0.21624227312463143 chrY 59373566 240443 0.004049664121572216 0.12388037687332291