BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054615.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 19,021,568 number of mapped reads = 15,364,061 (80.77%) number of supplementary alignments = 1,717 (0.01%) number of secondary alignments = 0 number of mapped bases = 714,514,075 bp number of sequenced bases = 714,350,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,486,163 duplication rate = 11.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3987 >>>>>>> ACTG content number of A's = 213,381,145 bp (29.87%) number of C's = 145,754,767 bp (20.4%) number of T's = 205,535,766 bp (28.77%) number of G's = 149,512,923 bp (20.93%) number of N's = 166,115 bp (0.02%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 3,647,364 number of insertions = 38,846 mapped reads with insertion percentage = 0.25% number of deletions = 109,045 mapped reads with deletion percentage = 0.71% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.2308X std coverageData = 1.2513X There is a 10.94% of reference with a coverageData >= 1X There is a 4.25% of reference with a coverageData >= 2X There is a 2.24% of reference with a coverageData >= 3X There is a 1.38% of reference with a coverageData >= 4X There is a 0.92% of reference with a coverageData >= 5X There is a 0.65% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 68909941 0.27646848270039015 1.6442865637307922 chr2 243199373 55731101 0.22915807846264472 1.322785070125905 chr3 198022430 53228187 0.2687987769870312 1.2046952963046147 chr4 191154276 42855691 0.22419425762675588 1.1083078186370803 chr5 180915260 35213831 0.19464267967223992 0.9604922588275939 chr6 171115067 34631120 0.20238498343339922 1.174369295265106 chr7 159138663 50123748 0.3149690154177052 1.6414079225615525 chr8 146364022 32376885 0.22120794822104575 1.2040141884116025 chr9 141213431 33501025 0.23723681779249453 1.2432857398905726 chr10 135534747 31863619 0.23509557294558567 1.3776437917710507 chr11 135006516 32365395 0.23973209559751915 1.2317167671152989 chr12 133851895 29393768 0.2195991920771835 1.0576099846896536 chr13 115169878 21883059 0.1900067915327652 0.9699261206015042 chr14 107349540 14246639 0.13271262270895617 0.8783603818404544 chr15 102531392 20236852 0.1973722545383954 0.9839062406213582 chr16 90354753 16432011 0.18186105826663043 1.0593586418421 chr17 81195210 12814910 0.15782839899053158 0.8615368091661814 chr18 78077248 28260015 0.36194942475431513 1.689777277063764 chr19 59128983 14039921 0.23744567025615848 1.3809687631744807 chr20 63025520 13725563 0.21777786204699304 1.0687967900347062 chr21 48129895 8150488 0.16934356495064035 1.1162098781323697 chr22 51304566 7076801 0.13793706002697695 0.7979296566553539 chrMT 16571 49553 2.990344577877014 4.768386783730275 chrX 155270560 55636978 0.35832277541859836 1.5539610359343972 chrY 59373566 1766974 0.029760280863035917 0.4615890085235365