BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525144.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 938,705 number of mapped reads = 852,613 (90.83%) number of supplementary alignments = 22,798 (2.43%) number of secondary alignments = 0 number of mapped bases = 65,732,885 bp number of sequenced bases = 65,706,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,363 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4771 >>>>>>> ACTG content number of A's = 17,361,667 bp (26.42%) number of C's = 12,355,249 bp (18.8%) number of T's = 20,112,934 bp (30.61%) number of G's = 15,874,504 bp (24.16%) number of N's = 2,274 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 481,151 number of insertions = 5,388 mapped reads with insertion percentage = 0.62% number of deletions = 15,096 mapped reads with deletion percentage = 1.75% homopolymer indels = 43.55% >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 0.2334X There is a 1.95% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5181959 0.020790154821720586 0.3289596720280903 chr2 243199373 5716898 0.023507042511988714 0.32772592076671236 chr3 198022430 4412279 0.022281713238242757 0.15838826984759896 chr4 191154276 4344891 0.022729760960199498 0.16567702491770078 chr5 180915260 4028868 0.022269365226570716 0.1593951127433375 chr6 171115067 3832255 0.022395777690342136 0.17708364366636364 chr7 159138663 3694700 0.023216859626375017 0.33533950005684726 chr8 146364022 3449430 0.023567472066325153 0.290026196683284 chr9 141213431 2731860 0.0193456102628085 0.23094669955438943 chr10 135534747 3089083 0.02279181588762622 0.2510812858165184 chr11 135006516 2960736 0.02193031927436747 0.23999542652324446 chr12 133851895 2976653 0.022238407607154162 0.1590621990706863 chr13 115169878 2160963 0.018763265512880024 0.14436522992089135 chr14 107349540 2001818 0.01864766257964403 0.16111251263884663 chr15 102531392 1864593 0.01818558164118166 0.1424147693522026 chr16 90354753 1811132 0.020044678778547487 0.16029943148729625 chr17 81195210 1653300 0.020362038598089716 0.18224304522084037 chr18 78077248 1806133 0.023132641662779917 0.3784684218441361 chr19 59128983 1217171 0.020585014966349076 0.2575894938826992 chr20 63025520 1313167 0.020835480611663338 0.16046389501864303 chr21 48129895 869369 0.01806297312720088 0.1509638284337625 chr22 51304566 656826 0.01280248623485091 0.11974451113348096 chrMT 16571 2099 0.12666706897592178 0.38381392194697345 chrX 155270560 3795820 0.024446488761295123 0.20878649147497272 chrY 59373566 160882 0.002709657021442842 0.07244460076944634