BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617556.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 53,003,018 number of mapped reads = 52,222,108 (98.53%) number of supplementary alignments = 1,410,800 (2.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,290,195 number of mapped paired reads (second in pair) = 25,931,913 number of mapped paired reads (both in pair) = 51,756,322 number of mapped paired reads (singletons) = 465,786 number of mapped bases = 6,971,624,666 bp number of sequenced bases = 6,966,223,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,722,266 duplication rate = 25.86% >>>>>>> Insert size mean insert size = 184,939.3695 std insert size = 4,176,852.0414 median insert size = 269 >>>>>>> Mapping quality mean mapping quality = 53.331 >>>>>>> ACTG content number of A's = 2,008,158,671 bp (28.83%) number of C's = 1,318,633,870 bp (18.93%) number of T's = 2,091,186,650 bp (30.02%) number of G's = 1,547,970,781 bp (22.22%) number of N's = 273,265 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 77,664,107 number of insertions = 1,243,394 mapped reads with insertion percentage = 2.24% number of deletions = 2,861,025 mapped reads with deletion percentage = 5.26% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 2.252X std coverageData = 19.7992X There is a 35.85% of reference with a coverageData >= 1X There is a 27.5% of reference with a coverageData >= 2X There is a 21.74% of reference with a coverageData >= 3X There is a 17.78% of reference with a coverageData >= 4X There is a 14.71% of reference with a coverageData >= 5X There is a 12.35% of reference with a coverageData >= 6X There is a 10.45% of reference with a coverageData >= 7X There is a 8.92% of reference with a coverageData >= 8X There is a 7.66% of reference with a coverageData >= 9X There is a 6.62% of reference with a coverageData >= 10X There is a 5.75% of reference with a coverageData >= 11X There is a 5.01% of reference with a coverageData >= 12X There is a 4.39% of reference with a coverageData >= 13X There is a 3.85% of reference with a coverageData >= 14X There is a 3.4% of reference with a coverageData >= 15X There is a 3.01% of reference with a coverageData >= 16X There is a 2.67% of reference with a coverageData >= 17X There is a 2.37% of reference with a coverageData >= 18X There is a 2.11% of reference with a coverageData >= 19X There is a 1.89% of reference with a coverageData >= 20X There is a 1.69% of reference with a coverageData >= 21X There is a 1.52% of reference with a coverageData >= 22X There is a 1.36% of reference with a coverageData >= 23X There is a 1.23% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.9% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.75% of reference with a coverageData >= 29X There is a 0.68% of reference with a coverageData >= 30X There is a 0.62% of reference with a coverageData >= 31X There is a 0.56% of reference with a coverageData >= 32X There is a 0.51% of reference with a coverageData >= 33X There is a 0.47% of reference with a coverageData >= 34X There is a 0.43% of reference with a coverageData >= 35X There is a 0.39% of reference with a coverageData >= 36X There is a 0.36% of reference with a coverageData >= 37X There is a 0.33% of reference with a coverageData >= 38X There is a 0.31% of reference with a coverageData >= 39X There is a 0.28% of reference with a coverageData >= 40X There is a 0.26% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 547510637 2.1966269724960887 13.927512783877704 chr2 243199373 655769550 2.6964277987673926 26.306896265158205 chr3 198022430 478568991 2.4167413307674286 5.646676216472462 chr4 191154276 496574741 2.5977694634463737 17.659469767028636 chr5 180915260 332756531 1.839294988161861 5.245365057169828 chr6 171115067 534263393 3.1222463478332974 9.613480334026379 chr7 159138663 417760894 2.6251376386139427 15.937095614354641 chr8 146364022 395141883 2.6997200377562733 8.219654348093329 chr9 141213431 320461578 2.2693420571305287 35.127909507809875 chr10 135534747 356918677 2.6334108772859555 58.2384428443427 chr11 135006516 276119780 2.0452329871248587 14.173471675610513 chr12 133851895 318949608 2.382854631979622 10.640547467427535 chr13 115169878 205031307 1.7802511434456847 4.786825332620918 chr14 107349540 205299116 1.9124359172847876 5.441346325280243 chr15 102531392 209943214 2.047599373272919 6.541685247299449 chr16 90354753 107440063 1.1890914360642433 17.826075024800485 chr17 81195210 137462178 1.6929838348838557 17.04725389394776 chr18 78077248 210251943 2.6928708219838895 27.505813505605573 chr19 59128983 99139726 1.676668885037309 7.8992567499446835 chr20 63025520 152980788 2.427283233839245 7.500599104342398 chr21 48129895 80267631 1.6677291940902843 10.199936429224495 chr22 51304566 72673238 1.416506242348878 4.888483413039367 chrMT 16571 3680284 222.0918472029449 108.6905969353728 chrX 155270560 334494921 2.1542713634832 7.556072481180421 chrY 59373566 22163994 0.3732973357200745 25.275693138899218