BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004098.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 = 3,705,101 number of mapped reads = 3,208,857 (86.61%) number of supplementary alignments = 28,652 (0.77%) number of secondary alignments = 0 number of mapped bases = 219,490,839 bp number of sequenced bases = 219,404,099 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,485 duplication rate = 5.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9083 >>>>>>> ACTG content number of A's = 61,633,967 bp (28.09%) number of C's = 41,144,724 bp (18.75%) number of T's = 70,180,915 bp (31.99%) number of G's = 46,414,169 bp (21.15%) number of N's = 30,324 bp (0.01%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,988,682 number of insertions = 17,274 mapped reads with insertion percentage = 0.53% number of deletions = 51,655 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.0709X std coverageData = 0.6843X There is a 5.14% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 24897625 0.0998899216383497 1.512816073464399 chr2 243199373 23820126 0.09794484955353894 0.5932638333895284 chr3 198022430 8060739 0.04070619171777662 0.315625917071007 chr4 191154276 17417429 0.09111712991447808 0.4446954295552294 chr5 180915260 14648090 0.08096658070745387 0.3654600055975429 chr6 171115067 15961223 0.09327771820350571 0.5301075189912601 chr7 159138663 14482567 0.0910059612603381 1.0911119675522774 chr8 146364022 7330757 0.050085785426147965 0.5884539351318089 chr9 141213431 8479572 0.06004791428090151 0.46140408958426465 chr10 135534747 19687720 0.14525957686703025 1.076185910063849 chr11 135006516 7310131 0.05414650504720824 0.34512767932463895 chr12 133851895 2338131 0.017468045558861906 0.1892816393192111 chr13 115169878 6197647 0.053813089912277234 0.2970821576135743 chr14 107349540 1138704 0.010607441820430717 0.18823176987330228 chr15 102531392 3237982 0.031580396372654335 0.22843434062846676 chr16 90354753 9216963 0.10200861265151154 0.49627255671403175 chr17 81195210 1083030 0.013338594727447592 0.17272970116706374 chr18 78077248 1786311 0.02287876488679519 0.7004131475360643 chr19 59128983 1458037 0.024658584099104156 1.0311223514822965 chr20 63025520 4692476 0.07445358642023105 0.36620305248944957 chr21 48129895 802492 0.016673462512228628 0.2688204170953213 chr22 51304566 2973687 0.05796144927919281 0.3043929825900625 chrMT 16571 118356 7.142357129925774 4.629791206659327 chrX 155270560 21721755 0.1398961593234416 0.5327497984959217 chrY 59373566 629289 0.010598807556884826 0.26111868642207414