BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238077.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 = 1,557,119 number of mapped reads = 1,320,054 (84.78%) number of supplementary alignments = 4,728 (0.3%) number of secondary alignments = 0 number of mapped bases = 81,499,669 bp number of sequenced bases = 81,455,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,782 duplication rate = 4.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0748 >>>>>>> ACTG content number of A's = 20,184,713 bp (24.78%) number of C's = 14,194,692 bp (17.43%) number of T's = 26,081,007 bp (32.02%) number of G's = 20,858,707 bp (25.61%) number of N's = 136,253 bp (0.17%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 712,224 number of insertions = 7,021 mapped reads with insertion percentage = 0.53% number of deletions = 26,867 mapped reads with deletion percentage = 2.01% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.0263X std coverageData = 0.2725X There is a 2.26% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6810901 0.02732551266141078 0.3838725718694958 chr2 243199373 6474922 0.02662392554770279 0.39322764241473596 chr3 198022430 5027052 0.025386275686042233 0.18908332856827498 chr4 191154276 5745863 0.030058773050936093 0.21866810363522646 chr5 180915260 5088483 0.02812633384270625 0.19154621841586267 chr6 171115067 4616159 0.026976928922337388 0.23905301053370406 chr7 159138663 4637104 0.029138764349176415 0.3676910818281418 chr8 146364022 3675247 0.02511031706958695 0.2510423149201694 chr9 141213431 3287309 0.02327901090371496 0.29244745250781806 chr10 135534747 3402638 0.02510528167363606 0.2935066747546905 chr11 135006516 3372697 0.02498173495566688 0.23648538367057306 chr12 133851895 4330860 0.03235561214878579 0.2191554407653276 chr13 115169878 2281579 0.019810553242055183 0.16649249276659142 chr14 107349540 2207322 0.020562007065889617 0.18854661565070135 chr15 102531392 2822475 0.027527910671494637 0.19302505887285704 chr16 90354753 2696274 0.029840975825588277 0.2216808208225956 chr17 81195210 2339389 0.028811908978374462 0.21806858075102387 chr18 78077248 1650399 0.02113802730342135 0.4132864110591577 chr19 59128983 1503048 0.02541981823025774 0.3097196810743863 chr20 63025520 1749527 0.027759025232953254 0.1999093305521949 chr21 48129895 928216 0.019285643569345 0.1801920205470441 chr22 51304566 803597 0.01566326474723517 0.14674224828335872 chrMT 16571 21079 1.2720415183151288 1.6672718421283879 chrX 155270560 5722964 0.03685801094553919 0.25007910296786 chrY 59373566 304565 0.005129639678371348 0.14178256783059212