BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818815.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 = 583,459 number of mapped reads = 540,545 (92.64%) number of supplementary alignments = 4,704 (0.81%) number of secondary alignments = 0 number of mapped bases = 36,674,207 bp number of sequenced bases = 36,659,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,850 duplication rate = 23.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8405 >>>>>>> ACTG content number of A's = 10,417,855 bp (28.42%) number of C's = 7,833,542 bp (21.37%) number of T's = 10,589,144 bp (28.89%) number of G's = 7,816,326 bp (21.32%) number of N's = 2,288 bp (0.01%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 185,221 number of insertions = 5,161 mapped reads with insertion percentage = 0.94% number of deletions = 9,446 mapped reads with deletion percentage = 1.73% homopolymer indels = 41.37% >>>>>>> Coverage mean coverageData = 0.0118X std coverageData = 0.189X There is a 0.8% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 3025652 0.01213899483123053 0.24399882167460094 chr2 243199373 3253364 0.013377353567437035 0.28812744931151857 chr3 198022430 2525812 0.012755181319611116 0.15721753795475668 chr4 191154276 2430588 0.012715321105346343 0.16793032248876635 chr5 180915260 2283420 0.012621489198865812 0.15753457102284585 chr6 171115067 2143635 0.012527447393045756 0.16377054584825387 chr7 159138663 2019052 0.012687375663071897 0.17557746564626384 chr8 146364022 1896502 0.012957432940726377 0.17110408354813686 chr9 141213431 1553704 0.01100252284076293 0.15632788988972868 chr10 135534747 1797843 0.013264812454329516 0.20932170794744276 chr11 135006516 1783526 0.013210666068888112 0.17156489408061948 chr12 133851895 1644444 0.012285548889688861 0.1630903523571444 chr13 115169878 1173762 0.010191571098130363 0.13982262456492817 chr14 107349540 1125437 0.010483854891227294 0.15094758574171593 chr15 102531392 1040857 0.010151593377372658 0.1403169660956198 chr16 90354753 1094971 0.01211857665085975 0.2141438219907365 chr17 81195210 965028 0.011885282395353126 0.1587104029044885 chr18 78077248 995605 0.012751538066505622 0.1928819263657957 chr19 59128983 709527 0.011999648294306026 0.21126398232504762 chr20 63025520 792371 0.012572224711513685 0.16114793329297944 chr21 48129895 479979 0.00997257525702061 0.1430736033178992 chr22 51304566 430823 0.008397361747490468 0.13586421910086022 chrMT 16571 26333 1.5891014422786796 2.357877498358882 chrX 155270560 1120942 0.007219282264455026 0.1221543042576524 chrY 59373566 361030 0.006080652120507635 0.30813242664077495