BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093990.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 = 309,640 number of mapped reads = 294,635 (95.15%) number of supplementary alignments = 19,010 (6.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 148,181 number of mapped paired reads (second in pair) = 146,454 number of mapped paired reads (both in pair) = 291,690 number of mapped paired reads (singletons) = 2,945 number of mapped bases = 37,468,265 bp number of sequenced bases = 36,807,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 275,129 duplication rate = 48.87% >>>>>>> Insert size mean insert size = 1,004,056.5271 std insert size = 9,115,276.2501 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 40.5325 >>>>>>> ACTG content number of A's = 9,720,519 bp (26.41%) number of C's = 8,637,842 bp (23.47%) number of T's = 9,164,122 bp (24.9%) number of G's = 9,284,354 bp (25.22%) number of N's = 438 bp (0%) GC percentage = 48.69% >>>>>>> Mismatches and indels general error rate = 0.0352 number of mismatches = 1,250,313 number of insertions = 19,994 mapped reads with insertion percentage = 6.66% number of deletions = 99,326 mapped reads with deletion percentage = 32.37% homopolymer indels = 29.17% >>>>>>> Coverage mean coverageData = 0.0121X std coverageData = 2.3174X 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% 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 805638 0.003232240693193699 1.0022258511320572 chr2 243199373 2095271 0.008615445731432868 2.572698738478721 chr3 198022430 681958 0.0034438421950483086 1.052595896137089 chr4 191154276 875511 0.004580127728871731 1.4910203088414835 chr5 180915260 381013 0.002106030193362351 1.1036091969000688 chr6 171115067 758609 0.004433326727447093 1.2881086187047874 chr7 159138663 601959 0.0037826068703367202 1.147336394261444 chr8 146364022 403438 0.0027564014331336152 0.81855451370846 chr9 141213431 467271 0.0033089699520154 0.9161295525397429 chr10 135534747 597016 0.00440489256972605 1.2877655118588502 chr11 135006516 1002770 0.007427567422005024 1.823134880331735 chr12 133851895 838640 0.006265432401984298 1.5032728775632618 chr13 115169878 828419 0.007193017952141965 1.8736924839782205 chr14 107349540 139172 0.0012964377863193452 0.39891551431717115 chr15 102531392 476000 0.004642480617058237 1.250326265171961 chr16 90354753 227638 0.002519380469115997 0.7033802050110158 chr17 81195210 898262 0.011062992509040866 2.6394472383343803 chr18 78077248 194119 0.002486242855280965 0.7339965652477403 chr19 59128983 165540 0.0027996422668050964 0.7406186866315124 chr20 63025520 321395 0.005099442257675938 1.6109911834848503 chr21 48129895 89543 0.0018604445324470374 0.36319487975316533 chr22 51304566 135005 0.0026314421995110534 0.7008648439757678 chrMT 16571 670475 40.46074467443123 204.17392073800082 chrX 155270560 23235369 0.14964439491942322 7.997021285517798 chrY 59373566 578234 0.009738913104865556 1.3106259179651527