BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093980.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 = 402,900 number of mapped reads = 382,058 (94.83%) number of supplementary alignments = 22,774 (5.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 192,220 number of mapped paired reads (second in pair) = 189,838 number of mapped paired reads (both in pair) = 378,174 number of mapped paired reads (singletons) = 3,884 number of mapped bases = 48,496,442 bp number of sequenced bases = 47,599,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 358,874 duplication rate = 49.65% >>>>>>> Insert size mean insert size = 988,207.629 std insert size = 9,033,562.7336 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 40.7302 >>>>>>> ACTG content number of A's = 12,720,802 bp (26.72%) number of C's = 11,020,232 bp (23.15%) number of T's = 11,951,085 bp (25.11%) number of G's = 11,906,663 bp (25.01%) number of N's = 689 bp (0%) GC percentage = 48.17% >>>>>>> Mismatches and indels general error rate = 0.0361 number of mismatches = 1,657,156 number of insertions = 27,585 mapped reads with insertion percentage = 7.09% number of deletions = 133,644 mapped reads with deletion percentage = 33.6% homopolymer indels = 29.5% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 2.817X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% 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 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 886126 0.0035551606509337443 1.1291556580046342 chr2 243199373 2071328 0.008516995642089915 2.6556691766469425 chr3 198022430 796425 0.00402189287344873 1.1706903039697505 chr4 191154276 1011606 0.005292091922652046 1.6574707218016902 chr5 180915260 483180 0.002670753147081125 1.3423626247320517 chr6 171115067 929357 0.005431181580287141 1.496989526856039 chr7 159138663 1169283 0.007347573354942664 2.110909337200898 chr8 146364022 515487 0.0035219515899884194 1.0683305056988193 chr9 141213431 705282 0.004994439941056315 1.483547230817028 chr10 135534747 903954 0.006669536926940218 1.9147326376211826 chr11 135006516 1050245 0.007779217115713141 1.8687367038145153 chr12 133851895 1085550 0.008110083163185698 1.955460116176223 chr13 115169878 883606 0.00767219706527778 1.9781646153195918 chr14 107349540 174933 0.0016295645048874919 0.5435198199385062 chr15 102531392 715244 0.006975853795099163 1.9189513801540903 chr16 90354753 277712 0.003073573783108012 0.8803453308628977 chr17 81195210 1047258 0.012898026866363176 3.025930915807045 chr18 78077248 280517 0.003592813619660365 0.9097603058522505 chr19 59128983 179472 0.0030352627576902516 0.81971321450938 chr20 63025520 322603 0.005118609096759535 1.516826058123548 chr21 48129895 113218 0.0023523425513394536 0.4403902215730849 chr22 51304566 154336 0.003008231275165645 0.6744824030759784 chrMT 16571 807594 48.735381087441915 209.67773019049486 chrX 155270560 31275794 0.2014277143072067 9.989232420602109 chrY 59373566 656332 0.011054279609885653 1.5231602877474508