BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237255.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 = 2,995,040 number of mapped reads = 2,684,112 (89.62%) number of supplementary alignments = 35,275 (1.18%) number of secondary alignments = 0 number of mapped bases = 165,726,358 bp number of sequenced bases = 165,646,682 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 972,452 duplication rate = 22.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2261 >>>>>>> ACTG content number of A's = 42,695,382 bp (25.77%) number of C's = 28,472,335 bp (17.19%) number of T's = 55,344,471 bp (33.41%) number of G's = 39,117,030 bp (23.61%) number of N's = 17,464 bp (0.01%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 1,143,858 number of insertions = 16,922 mapped reads with insertion percentage = 0.62% number of deletions = 43,325 mapped reads with deletion percentage = 1.59% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.8844X There is a 1.83% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.1% 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 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% 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 11547325 0.04632816942911448 0.6200505854521576 chr2 243199373 9833169 0.040432542562517215 1.525604956400518 chr3 198022430 15705879 0.07931363633907533 0.6335792945100172 chr4 191154276 7963030 0.04165760853814225 0.9419549080321215 chr5 180915260 7433412 0.04108781094530113 0.45373908072648794 chr6 171115067 17298010 0.10108992915276128 0.8395330723153475 chr7 159138663 7759938 0.04876211634378253 0.5975933797717734 chr8 146364022 10294817 0.0703370736833127 1.855653767803801 chr9 141213431 6944121 0.04917464968328685 0.5897707375707337 chr10 135534747 8296674 0.06121436888800184 1.267387582843787 chr11 135006516 7861627 0.058231463435438925 0.6067233382247593 chr12 133851895 4686038 0.03500912706540315 0.4381472392700499 chr13 115169878 6095959 0.052930150711803306 0.5524148385156354 chr14 107349540 5713356 0.05322198865500495 0.5281208661297097 chr15 102531392 4358675 0.042510639083101494 0.4725520955179267 chr16 90354753 3680266 0.04073129390326594 0.529629576778178 chr17 81195210 5676443 0.06991105756115416 0.6741976934335882 chr18 78077248 5920528 0.07582910709147946 1.3660221957933136 chr19 59128983 2653730 0.04488035926476192 0.5245086227370186 chr20 63025520 3890474 0.06172855059347388 0.6061197289636873 chr21 48129895 3099591 0.06440053525984214 0.7672489187158019 chr22 51304566 1206677 0.02351987540446205 0.32321425123391084 chrMT 16571 7395 0.4462615412467564 1.1798211359815134 chrX 155270560 6814641 0.043888815754899065 0.49637906439804896 chrY 59373566 984583 0.016582851028351574 0.8306919680876795