BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819018.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,568,827 number of mapped reads = 2,425,289 (94.41%) number of supplementary alignments = 24,220 (0.94%) number of secondary alignments = 0 number of mapped bases = 225,433,218 bp number of sequenced bases = 225,305,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,044,198 duplication rate = 33.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2713 >>>>>>> ACTG content number of A's = 63,717,121 bp (28.28%) number of C's = 44,975,771 bp (19.96%) number of T's = 64,333,251 bp (28.55%) number of G's = 52,268,509 bp (23.2%) number of N's = 10,965 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,428,255 number of insertions = 34,312 mapped reads with insertion percentage = 1.37% number of deletions = 67,594 mapped reads with deletion percentage = 2.72% homopolymer indels = 40.84% >>>>>>> Coverage mean coverageData = 0.0728X std coverageData = 1.0059X There is a 3.41% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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% 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 23545929 0.09446688199023584 1.934370878728859 chr2 243199373 18651713 0.07669309657307381 1.31557366888223 chr3 198022430 12349856 0.06236594511035947 0.47410380131305496 chr4 191154276 12637981 0.0661140376477898 0.5869210602165673 chr5 180915260 13057647 0.07217548702082953 0.5297220912705625 chr6 171115067 9516496 0.05561459996973849 0.6146457943866339 chr7 159138663 10920796 0.06862440461750015 1.3851804366232414 chr8 146364022 20595295 0.14071282490447004 0.8392577389754762 chr9 141213431 9931788 0.07033175194220725 1.0768676185073698 chr10 135534747 12176772 0.08984243723124373 1.1924120807672738 chr11 135006516 7901437 0.058526338091711066 0.6517568902911687 chr12 133851895 10397630 0.0776801105430745 0.5415188397358922 chr13 115169878 4846663 0.04208273104187885 0.3790776647817209 chr14 107349540 5181614 0.04826861857069904 0.48503158324348045 chr15 102531392 5941663 0.05794969603065567 0.45632339093833624 chr16 90354753 7437631 0.08231587994048305 1.0125825882228692 chr17 81195210 8085088 0.09957592325951248 0.7761232292707995 chr18 78077248 5357536 0.06861840212400928 1.237053118502886 chr19 59128983 5002918 0.08461024942708723 1.8381007244395338 chr20 63025520 7443657 0.11810544363616517 0.7235784392384219 chr21 48129895 3150379 0.06545576299304205 0.5540644986021698 chr22 51304566 1869670 0.036442565365429655 0.3957229073084239 chrMT 16571 148343 8.951964274938145 7.643727485175474 chrX 155270560 8528040 0.05492374085596136 0.6444403733789159 chrY 59373566 756676 0.01274432463766788 0.8563377953267632