BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094024.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 474,992 number of mapped reads = 442,617 (93.18%) number of supplementary alignments = 22,847 (4.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 222,579 number of mapped paired reads (second in pair) = 220,038 number of mapped paired reads (both in pair) = 436,730 number of mapped paired reads (singletons) = 5,887 number of mapped bases = 57,355,919 bp number of sequenced bases = 56,077,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 414,853 duplication rate = 45.74% >>>>>>> Insert size mean insert size = 470,427.0524 std insert size = 6,294,096.8297 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 44.8932 >>>>>>> ACTG content number of A's = 15,518,325 bp (27.67%) number of C's = 12,533,581 bp (22.35%) number of T's = 14,903,490 bp (26.58%) number of G's = 13,121,145 bp (23.4%) number of N's = 539 bp (0%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.0393 number of mismatches = 2,146,909 number of insertions = 34,007 mapped reads with insertion percentage = 7.53% number of deletions = 154,453 mapped reads with deletion percentage = 33.71% homopolymer indels = 27.56% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 6.1548X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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% 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 706103 0.0028329036740895423 0.6821663504220711 chr2 243199373 3092431 0.012715620775880865 3.72444776022928 chr3 198022430 1227552 0.0061990553292371985 1.8252076280120726 chr4 191154276 530345 0.002774434405014304 0.5775439966937395 chr5 180915260 1011459 0.005590788748279167 1.8530547102681947 chr6 171115067 1764044 0.010309109717380995 4.248535698684018 chr7 159138663 1334488 0.00838569317375753 2.3683752931555757 chr8 146364022 1436876 0.009817139351363274 2.6814203474006404 chr9 141213431 1034632 0.007326725175312822 2.8449616925719554 chr10 135534747 856668 0.006320652223595474 1.3198996209895277 chr11 135006516 1549974 0.011480734752091522 2.8053207267099687 chr12 133851895 2121026 0.015846066280944322 4.145855236606075 chr13 115169878 619294 0.005377221985074952 1.6759094468020541 chr14 107349540 242812 0.0022618820723405058 0.457592208432206 chr15 102531392 813540 0.00793454554874277 2.21874752643755 chr16 90354753 352206 0.0038980351149872547 1.1044640218961717 chr17 81195210 1709461 0.02105371733135489 5.159503275698373 chr18 78077248 357366 0.004577082429954499 1.2578868369479554 chr19 59128983 363037 0.0061397470678634875 1.2887175743189168 chr20 63025520 478626 0.007594161856974762 2.9644388168805738 chr21 48129895 373428 0.007758753681054156 2.3571888316516496 chr22 51304566 166669 0.0032486192359565034 0.5125868744630998 chrMT 16571 8133048 490.8000724156659 2073.6854033801374 chrX 155270560 26682712 0.17184656254218442 12.210192566360691 chrY 59373566 398122 0.0067053745769624145 1.2010062070824132