BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514742.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 79,555,125 number of mapped reads = 78,132,324 (98.21%) number of supplementary alignments = 2,040,442 (2.56%) number of secondary alignments = 0 number of mapped bases = 7,477,719,782 bp number of sequenced bases = 7,473,916,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,915,250 duplication rate = 42.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2702 >>>>>>> ACTG content number of A's = 1,917,556,444 bp (25.66%) number of C's = 1,786,231,409 bp (23.9%) number of T's = 1,939,498,778 bp (25.95%) number of G's = 1,790,756,282 bp (23.96%) number of N's = 39,873,913 bp (0.53%) GC percentage = 47.86% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 58,583,461 number of insertions = 2,542,408 mapped reads with insertion percentage = 3.15% number of deletions = 1,952,436 mapped reads with deletion percentage = 2.43% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 2.4155X std coverageData = 35.8595X There is a 10.83% of reference with a coverageData >= 1X There is a 6.87% of reference with a coverageData >= 2X There is a 5.17% of reference with a coverageData >= 3X There is a 4.32% of reference with a coverageData >= 4X There is a 3.78% of reference with a coverageData >= 5X There is a 3.42% of reference with a coverageData >= 6X There is a 3.14% of reference with a coverageData >= 7X There is a 2.93% of reference with a coverageData >= 8X There is a 2.76% of reference with a coverageData >= 9X There is a 2.61% of reference with a coverageData >= 10X There is a 2.49% of reference with a coverageData >= 11X There is a 2.38% of reference with a coverageData >= 12X There is a 2.28% of reference with a coverageData >= 13X There is a 2.2% of reference with a coverageData >= 14X There is a 2.12% of reference with a coverageData >= 15X There is a 2.05% of reference with a coverageData >= 16X There is a 1.99% of reference with a coverageData >= 17X There is a 1.93% of reference with a coverageData >= 18X There is a 1.87% of reference with a coverageData >= 19X There is a 1.82% of reference with a coverageData >= 20X There is a 1.77% of reference with a coverageData >= 21X There is a 1.72% of reference with a coverageData >= 22X There is a 1.68% of reference with a coverageData >= 23X There is a 1.64% of reference with a coverageData >= 24X There is a 1.6% of reference with a coverageData >= 25X There is a 1.57% of reference with a coverageData >= 26X There is a 1.53% of reference with a coverageData >= 27X There is a 1.5% of reference with a coverageData >= 28X There is a 1.47% of reference with a coverageData >= 29X There is a 1.44% of reference with a coverageData >= 30X There is a 1.41% of reference with a coverageData >= 31X There is a 1.38% of reference with a coverageData >= 32X There is a 1.35% of reference with a coverageData >= 33X There is a 1.33% of reference with a coverageData >= 34X There is a 1.3% of reference with a coverageData >= 35X There is a 1.28% of reference with a coverageData >= 36X There is a 1.26% of reference with a coverageData >= 37X There is a 1.23% of reference with a coverageData >= 38X There is a 1.21% of reference with a coverageData >= 39X There is a 1.19% of reference with a coverageData >= 40X There is a 1.17% of reference with a coverageData >= 41X There is a 1.15% of reference with a coverageData >= 42X There is a 1.13% of reference with a coverageData >= 43X There is a 1.11% of reference with a coverageData >= 44X There is a 1.1% of reference with a coverageData >= 45X There is a 1.08% of reference with a coverageData >= 46X There is a 1.06% of reference with a coverageData >= 47X There is a 1.05% of reference with a coverageData >= 48X There is a 1.03% of reference with a coverageData >= 49X There is a 1.01% of reference with a coverageData >= 50X There is a 1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 384990038 1.5445900854947117 22.90719031603153 chr2 243199373 1154751770 4.748169190386852 68.37525513829533 chr3 198022430 649077900 3.277799893678711 27.269616131523723 chr4 191154276 545468414 2.8535506786152145 30.521431081511338 chr5 180915260 335680259 1.855455747624606 18.12991151376863 chr6 171115067 232034349 1.356013547304984 26.323591796022285 chr7 159138663 506536268 3.182986827028954 33.1726816560092 chr8 146364022 310968095 2.12462113811002 25.858138240204553 chr9 141213431 136638852 0.96760521313302 17.03329436951338 chr10 135534747 193455782 1.4273519247429591 23.12345955841874 chr11 135006516 670569921 4.966944862127988 58.03244909557234 chr12 133851895 257170257 1.9213045657665138 27.74263383573308 chr13 115169878 58410479 0.5071680200963659 12.601059292812675 chr14 107349540 188056580 1.7518154246399193 31.772216397838662 chr15 102531392 198532156 1.9363060632201308 48.37205988323055 chr16 90354753 174038742 1.9261714101526015 28.52820319111567 chr17 81195210 266705595 3.284745430179933 25.90636179967421 chr18 78077248 96134124 1.231269370559782 19.861365603793793 chr19 59128983 591434964 10.002454532323007 62.466142299630015 chr20 63025520 102560651 1.6272876606174769 44.12740867758949 chr21 48129895 293446392 6.096967217568208 84.21931512332435 chr22 51304566 68038499 1.3261684934631355 17.73081349771985 chrMT 16571 6796838 410.1646249471969 198.59756911452345 chrX 155270560 40109154 0.2583178292137286 4.773789509475883 chrY 59373566 16113703 0.27139523672874893 14.790319956976665