BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046545.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,690,830 number of mapped reads = 7,546,991 (98.13%) number of supplementary alignments = 33,184 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,831,558 number of mapped paired reads (second in pair) = 3,715,433 number of mapped paired reads (both in pair) = 7,419,162 number of mapped paired reads (singletons) = 127,829 number of mapped bases = 704,068,626 bp number of sequenced bases = 703,892,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,063,375 duplication rate = 42.56% >>>>>>> Insert size mean insert size = 27,017.8817 std insert size = 1,667,916.1202 median insert size = 127 >>>>>>> Mapping quality mean mapping quality = 53.1452 >>>>>>> ACTG content number of A's = 206,826,484 bp (29.38%) number of C's = 145,274,751 bp (20.64%) number of T's = 204,504,744 bp (29.05%) number of G's = 147,222,907 bp (20.92%) number of N's = 63,479 bp (0.01%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 2,486,690 number of insertions = 54,874 mapped reads with insertion percentage = 0.71% number of deletions = 65,815 mapped reads with deletion percentage = 0.85% homopolymer indels = 48.21% >>>>>>> Coverage mean coverageData = 0.2274X std coverageData = 14.1067X There is a 2.79% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 97844718 0.39255556358272825 18.54037803419046 chr2 243199373 61570940 0.2531706362581782 12.813238030308025 chr3 198022430 42653085 0.21539522063232938 11.925540695597196 chr4 191154276 15085940 0.07892023299546802 3.8329053917938705 chr5 180915260 58734570 0.32465238145195713 20.72757366520853 chr6 171115067 43433666 0.25382724479779445 11.30605495722207 chr7 159138663 43144770 0.27111431745533765 14.632465319050224 chr8 146364022 86160266 0.588671073824413 31.60100567256451 chr9 141213431 16307765 0.11548310160384107 9.694366394094763 chr10 135534747 29299720 0.21617866007452688 13.809500857576952 chr11 135006516 26754657 0.19817307929048403 10.447551693422433 chr12 133851895 18759964 0.14015463882674206 7.05416496797974 chr13 115169878 15726335 0.13654902890493642 6.641339830047888 chr14 107349540 33885517 0.315655912451977 18.79390672021661 chr15 102531392 13114389 0.1279060855820625 6.126702881914289 chr16 90354753 30362087 0.336031984947156 21.1371991574483 chr17 81195210 22465542 0.2766855581751682 11.019776931880157 chr18 78077248 5619861 0.07197821572809533 3.169271041553016 chr19 59128983 7848493 0.13273512585190245 6.268199880481306 chr20 63025520 14208775 0.22544478807949542 12.388004968777791 chr21 48129895 3137856 0.06519557127643848 5.493640946584536 chr22 51304566 3389552 0.06606725802923662 2.4938816214991006 chrMT 16571 46193 2.787580713294309 2.429257181496614 chrX 155270560 14356600 0.09246182920960677 6.918909344213891 chrY 59373566 157365 0.0026504219066107635 0.16130237928451677