BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081052.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,531,739 number of mapped reads = 1,196,927 (78.14%) number of supplementary alignments = 5,992 (0.39%) number of secondary alignments = 0 number of mapped bases = 77,249,714 bp number of sequenced bases = 77,221,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,011 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7216 >>>>>>> ACTG content number of A's = 22,164,327 bp (28.7%) number of C's = 14,697,333 bp (19.03%) number of T's = 23,343,913 bp (30.23%) number of G's = 17,014,919 bp (22.03%) number of N's = 1,036 bp (0%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 576,675 number of insertions = 5,025 mapped reads with insertion percentage = 0.42% number of deletions = 16,265 mapped reads with deletion percentage = 1.34% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.2204X There is a 2.25% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6375636 0.025579218115568906 0.3133681741823269 chr2 243199373 6272194 0.025790337872293775 0.22999932277088891 chr3 198022430 5665828 0.028612051675156194 0.1823723132301025 chr4 191154276 5591718 0.029252382510135427 0.19069811110380636 chr5 180915260 4709662 0.026032419819090994 0.17424110767144374 chr6 171115067 4141213 0.02420133464927434 0.20221365889363516 chr7 159138663 4336715 0.027251171514492363 0.3215040599650999 chr8 146364022 3690019 0.02521124351174225 0.23131307785393718 chr9 141213431 3417178 0.024198675549495004 0.21013111831390693 chr10 135534747 3190842 0.023542612286722314 0.2052427444258303 chr11 135006516 3173389 0.02350545065543355 0.21552881487829778 chr12 133851895 3517776 0.026281107189405125 0.17580050481732817 chr13 115169878 2222572 0.019298205733968045 0.1491470812901142 chr14 107349540 2471761 0.023025352507332588 0.17037029947868926 chr15 102531392 2298412 0.02241666630255054 0.16617067610832384 chr16 90354753 2328868 0.025774714917321504 0.18358150103553791 chr17 81195210 1954816 0.024075508887777985 0.18867800876043828 chr18 78077248 2287929 0.02930340218958537 0.38093274234866 chr19 59128983 1189202 0.020111998205685357 0.24277884616166823 chr20 63025520 1712891 0.027177736891341793 0.18094357998469313 chr21 48129895 1115251 0.023171689861363712 0.1729902249242381 chr22 51304566 835482 0.016284749392480972 0.13668352199143716 chrMT 16571 12992 0.7840202763864583 1.0421683228629024 chrX 155270560 4546422 0.029280644057701602 0.20064450844446682 chrY 59373566 190946 0.003216010303305683 0.08089158915002383