BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094155.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 = 336,238 number of mapped reads = 299,958 (89.21%) number of supplementary alignments = 2,504 (0.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 150,539 number of mapped paired reads (second in pair) = 149,419 number of mapped paired reads (both in pair) = 297,932 number of mapped paired reads (singletons) = 2,026 number of mapped bases = 39,797,267 bp number of sequenced bases = 38,579,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 294,817 duplication rate = 43.01% >>>>>>> Insert size mean insert size = 118,797.6767 std insert size = 3,151,491.2106 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 29.7477 >>>>>>> ACTG content number of A's = 10,706,400 bp (27.75%) number of C's = 8,352,591 bp (21.65%) number of T's = 10,744,369 bp (27.85%) number of G's = 8,776,181 bp (22.75%) number of N's = 308 bp (0%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0487 number of mismatches = 1,910,825 number of insertions = 13,677 mapped reads with insertion percentage = 4.48% number of deletions = 170,040 mapped reads with deletion percentage = 52.05% homopolymer indels = 19.99% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 12.9387X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 812235 0.0032587080294576277 2.0529707443365495 chr2 243199373 1866800 0.0076760066318098605 4.950852758258142 chr3 198022430 1837811 0.00928082237956579 8.420068664265788 chr4 191154276 745464 0.00389980290056394 3.540665612726627 chr5 180915260 225040 0.0012438972809701073 0.9757643487897464 chr6 171115067 7997218 0.04673590783212562 34.46315888091901 chr7 159138663 395198 0.002483356291613434 1.1478217915480868 chr8 146364022 125669 8.586058122944995E-4 0.3631638165212273 chr9 141213431 615690 0.004359996040319989 2.666491464602084 chr10 135534747 198228 0.0014625622166100328 0.5425593695547605 chr11 135006516 42376 3.138811462996349E-4 0.15716021411111517 chr12 133851895 294165 0.0021976902157418094 1.8464422157985343 chr13 115169878 2928368 0.02542650952534655 22.916443447901838 chr14 107349540 925266 0.008619189239190033 5.002875319613667 chr15 102531392 983879 0.009595880645022356 7.300234419978741 chr16 90354753 696498 0.00770848214260516 3.6994069161867253 chr17 81195210 188326 0.002319422537363965 0.5648683618130879 chr18 78077248 64585 8.271936019056409E-4 0.39185055953681236 chr19 59128983 158807 0.0026857725592878876 1.0088526749423514 chr20 63025520 68120 0.0010808320185220208 0.5457755475608994 chr21 48129895 347027 0.007210217267251466 2.4774367175230436 chr22 51304566 575870 0.011224537012943448 4.6894333006811815 chrMT 16571 5580888 336.7864341319172 2159.7684545292486 chrX 155270560 12058728 0.07766268119339557 29.927311770358184 chrY 59373566 65011 0.0010949485499995065 0.4758414482540941