BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818974.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 = 3,374,901 number of mapped reads = 3,328,645 (98.63%) number of supplementary alignments = 46,511 (1.38%) number of secondary alignments = 0 number of mapped bases = 308,171,053 bp number of sequenced bases = 307,992,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,895,576 duplication rate = 46.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9758 >>>>>>> ACTG content number of A's = 89,614,711 bp (29.1%) number of C's = 66,066,118 bp (21.45%) number of T's = 87,364,987 bp (28.37%) number of G's = 64,931,187 bp (21.08%) number of N's = 15,187 bp (0%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,928,289 number of insertions = 44,221 mapped reads with insertion percentage = 1.29% number of deletions = 96,600 mapped reads with deletion percentage = 2.84% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0995X std coverageData = 1.1958X There is a 3.36% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 1.33% of reference with a coverageData >= 3X There is a 0.91% of reference with a coverageData >= 4X There is a 0.62% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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% 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 30770042 0.12345021198563032 2.0561391098153843 chr2 243199373 23855472 0.09809018709928993 1.683282954476337 chr3 198022430 16088384 0.08124526095351925 0.6414861237190891 chr4 191154276 17400171 0.09102684681769818 0.7738667066112053 chr5 180915260 16953485 0.09370953561352426 0.7184241581345167 chr6 171115067 12755974 0.07454617657952937 0.7974588136262207 chr7 159138663 15289351 0.09607565321822517 1.4546963106742665 chr8 146364022 28942313 0.1977419901729675 1.169757193814969 chr9 141213431 13466455 0.09536242342274086 1.1534072709882064 chr10 135534747 16140076 0.1190844145671368 1.438761209875423 chr11 135006516 10361469 0.0767479178560537 0.7716074919962352 chr12 133851895 14439853 0.10787933185406154 0.7667179490941577 chr13 115169878 6186729 0.05371829081906295 0.5202791977317948 chr14 107349540 7238549 0.06742971604722293 0.6282969237212579 chr15 102531392 7909118 0.07713850212820675 0.6402365260871721 chr16 90354753 9884186 0.10939309412975762 1.383560872946748 chr17 81195210 11013109 0.1356374224538615 0.9737833683350012 chr18 78077248 6790641 0.08697336514729617 1.3143969468528522 chr19 59128983 6314620 0.10679398967508033 1.8419817601277542 chr20 63025520 8756727 0.1389393851887299 0.9108512939272151 chr21 48129895 4258204 0.08847316205447778 0.7409310151792169 chr22 51304566 2406311 0.046902472579146266 0.5255146857650033 chrMT 16571 1071623 64.66857763562851 41.73605894025559 chrX 155270560 18751404 0.12076599710853107 0.9419839463392772 chrY 59373566 1126787 0.018977923609978218 1.2183866624211077