BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068113.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 = 2,437,196 number of mapped reads = 1,795,456 (73.67%) number of supplementary alignments = 16,000 (0.66%) number of secondary alignments = 0 number of mapped bases = 117,799,365 bp number of sequenced bases = 117,753,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,723 duplication rate = 13.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6129 >>>>>>> ACTG content number of A's = 32,426,524 bp (27.54%) number of C's = 20,805,270 bp (17.67%) number of T's = 38,381,011 bp (32.59%) number of G's = 26,004,734 bp (22.08%) number of N's = 136,416 bp (0.12%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,017,136 number of insertions = 8,738 mapped reads with insertion percentage = 0.48% number of deletions = 27,825 mapped reads with deletion percentage = 1.53% homopolymer indels = 48% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.5479X There is a 1.31% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 9557179 0.03834365170949765 0.8794735616711041 chr2 243199373 7784891 0.032010325125303676 0.523499303195316 chr3 198022430 10301427 0.052021515946451116 0.5585189906779229 chr4 191154276 6637658 0.03472408851581222 0.45424842383743286 chr5 180915260 8529269 0.047145105393541706 0.5226829616981449 chr6 171115067 7061577 0.041268002425525745 0.5137080069377257 chr7 159138663 6222961 0.03910401710488167 0.5991116716095205 chr8 146364022 5939280 0.04057882476063687 0.6583839751448317 chr9 141213431 3793238 0.02686173668565563 0.4166406989953519 chr10 135534747 5330161 0.03932689674036135 0.5218318978142303 chr11 135006516 4278587 0.03169170738396064 0.4400834107220208 chr12 133851895 4215125 0.03149096245518227 0.42948583472702945 chr13 115169878 3606276 0.03131266666792857 0.4308381199628766 chr14 107349540 3722767 0.03467892829349804 0.4421082323688893 chr15 102531392 4788810 0.046705793285240875 0.5225995970163284 chr16 90354753 2307559 0.02553887784962458 0.37856207975165873 chr17 81195210 3485095 0.042922421162529166 0.4803208294003648 chr18 78077248 2853001 0.03654074744027863 0.5986830444958513 chr19 59128983 2579870 0.04363122565459988 0.6301460609234198 chr20 63025520 2914095 0.04623674663850453 0.5135440186344065 chr21 48129895 1539325 0.0319827209263598 0.4246475941508724 chr22 51304566 1074926 0.020951858358961656 0.3176127751238513 chrMT 16571 7001 0.42248506426890353 1.1936706247452789 chrX 155270560 8945487 0.057612254377133694 0.5982011613240649 chrY 59373566 323800 0.005453605397391829 0.16240631940432051