BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237798.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 = 3,904,478 number of mapped reads = 3,400,272 (87.09%) number of supplementary alignments = 32,211 (0.82%) number of secondary alignments = 0 number of mapped bases = 241,112,661 bp number of sequenced bases = 241,012,454 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 548,903 duplication rate = 12.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8561 >>>>>>> ACTG content number of A's = 71,290,374 bp (29.58%) number of C's = 46,522,962 bp (19.3%) number of T's = 73,471,190 bp (30.48%) number of G's = 49,322,282 bp (20.46%) number of N's = 405,646 bp (0.17%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,968,185 number of insertions = 18,065 mapped reads with insertion percentage = 0.53% number of deletions = 55,647 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.0779X std coverageData = 1.1686X There is a 1.5% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 21272404 0.08534544032289493 1.8450519628805166 chr2 243199373 21643836 0.08899626562770785 1.1845221412733145 chr3 198022430 19259306 0.09725820453773848 1.1623660776708193 chr4 191154276 17930762 0.09380256814134778 1.1101864829121977 chr5 180915260 13031510 0.07203101606796464 0.9503379545248163 chr6 171115067 13191591 0.07709193136101802 1.0299366828137322 chr7 159138663 12543318 0.07882005392994913 1.2710537971455902 chr8 146364022 12040538 0.08226432859299261 1.2430172814497351 chr9 141213431 9562060 0.06771353073348951 1.0319862090978555 chr10 135534747 10980450 0.08101575605553017 1.240372554748878 chr11 135006516 10371429 0.07682169207299594 1.0698887653864235 chr12 133851895 10541900 0.07875794362119416 1.015534139406499 chr13 115169878 8042578 0.06983230458922601 0.9604928975320465 chr14 107349540 6741999 0.06280417223958296 0.9399942570645609 chr15 102531392 7131882 0.06955803350450952 0.9462964470238792 chr16 90354753 6542443 0.07240839892506817 0.9841868754755021 chr17 81195210 5629836 0.06933704586760721 0.9318351902497388 chr18 78077248 6619158 0.08477704029732196 1.628748190551131 chr19 59128983 3635410 0.06148270806551839 1.174868233181378 chr20 63025520 4675126 0.07417830110723402 1.00725439300175 chr21 48129895 2780546 0.05777170301327273 0.8223873543506078 chr22 51304566 2151136 0.041928743730138954 0.6830316327642209 chrMT 16571 24761 1.4942369199203427 3.3628377246953467 chrX 155270560 14092286 0.09075954900916182 1.094528168737771 chrY 59373566 676396 0.011392207771384322 0.36817211909749986