BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708541.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 23,174,906 number of mapped reads = 22,374,858 (96.55%) number of supplementary alignments = 547 (0%) number of secondary alignments = 0 number of mapped bases = 1,115,868,570 bp number of sequenced bases = 1,115,775,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,491 duplication rate = 0.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3552 >>>>>>> ACTG content number of A's = 344,240,109 bp (30.85%) number of C's = 211,657,124 bp (18.97%) number of T's = 343,979,921 bp (30.83%) number of G's = 215,517,646 bp (19.32%) number of N's = 380,398 bp (0.03%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,705,431 number of insertions = 58,865 mapped reads with insertion percentage = 0.26% number of deletions = 56,342 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 0.3605X std coverageData = 0.6659X There is a 27.67% of reference with a coverageData >= 1X There is a 6.64% of reference with a coverageData >= 2X There is a 1.4% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.01% 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 85547918 0.3432204808829744 0.6618979774575826 chr2 243199373 103396569 0.42515146204756044 0.7096577409514119 chr3 198022430 86376555 0.43619581377725747 0.7139703555977063 chr4 191154276 92946934 0.4862404124300102 0.7521838697335695 chr5 180915260 80135056 0.44294249141835795 0.7209549970260888 chr6 171115067 75874818 0.44341400982532997 0.7242155764231558 chr7 159138663 64031639 0.402363811489355 0.6993273289598623 chr8 146364022 62409897 0.4264018995050573 0.7089720738394432 chr9 141213431 46406822 0.3286289531482314 0.6434396707179209 chr10 135534747 47641427 0.351507108357977 0.6439373666237383 chr11 135006516 49762365 0.368592320388447 0.6728132700216682 chr12 133851895 51528447 0.3849661373864001 0.685129499525252 chr13 115169878 47085999 0.40883953180882937 0.7110422808924176 chr14 107349540 35634562 0.331948902622219 0.6471265954139138 chr15 102531392 29961433 0.29221716798695174 0.6095753742825256 chr16 90354753 20084863 0.22228894809772762 0.5234534286991779 chr17 81195210 17696189 0.2179462187486183 0.5231905241375502 chr18 78077248 33808025 0.4330073851988226 0.7159473698816222 chr19 59128983 7772480 0.1314495803183356 0.39417608017615396 chr20 63025520 17011374 0.2699124735503967 0.5784148569242729 chr21 48129895 14273046 0.2965526103890316 0.6311476006204213 chr22 51304566 5625012 0.10963959815974274 0.3663261163351184 chrMT 16571 921 0.055579023595437815 0.22910695260427077 chrX 155270560 35780771 0.23044143719195706 0.505252091319884 chrY 59373566 5075448 0.08548329403020866 0.32744935206846676