BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714096.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 523,720 number of mapped reads = 424,740 (81.1%) number of supplementary alignments = 14,814 (2.83%) number of secondary alignments = 0 number of mapped bases = 55,315,216 bp number of sequenced bases = 53,935,330 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 369,288 duplication rate = 42.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2406 >>>>>>> ACTG content number of A's = 15,217,816 bp (28.21%) number of C's = 11,091,773 bp (20.56%) number of T's = 14,382,476 bp (26.67%) number of G's = 13,242,922 bp (24.55%) number of N's = 343 bp (0%) GC percentage = 45.12% >>>>>>> Mismatches and indels general error rate = 0.0483 number of mismatches = 2,446,984 number of insertions = 61,375 mapped reads with insertion percentage = 13.9% number of deletions = 218,814 mapped reads with deletion percentage = 47.77% homopolymer indels = 30.01% >>>>>>> Coverage mean coverageData = 0.0179X std coverageData = 3.4256X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4042903 0.016220232406161186 2.846536750406543 chr2 243199373 5862265 0.02410477020432121 7.76381361183004 chr3 198022430 2808923 0.014184872895459368 1.9355864087071069 chr4 191154276 2298722 0.01202548040306459 1.8162922324042503 chr5 180915260 3520272 0.01945812641785994 3.3787011847618817 chr6 171115067 2621828 0.015322017201442582 2.4285122337575946 chr7 159138663 2524947 0.01586633287223231 2.2300516973126374 chr8 146364022 3118677 0.021307674914809324 3.864853816934031 chr9 141213431 2293989 0.016244835804605583 2.4913462699820315 chr10 135534747 2768724 0.02042814895282905 3.7489952337838437 chr11 135006516 2869394 0.021253744522968063 3.4742640268350393 chr12 133851895 1696707 0.012676002831338323 1.990931080107359 chr13 115169878 2021713 0.017554182005819263 2.909275584571696 chr14 107349540 2273601 0.02117942005154377 3.158895900450719 chr15 102531392 1142889 0.011146722751993849 1.2794057962788556 chr16 90354753 1225734 0.013565794374978813 1.7806126656743975 chr17 81195210 1638635 0.02018142449536124 3.1544278165357316 chr18 78077248 1293926 0.01657238226429292 1.9865839206682945 chr19 59128983 871725 0.01474277005576098 1.688048517082474 chr20 63025520 1068523 0.016953814899107536 2.267487866882759 chr21 48129895 399763 0.008305918805765106 1.268433536901109 chr22 51304566 845958 0.016488941744483326 3.2676670807125743 chrMT 16571 467994 28.24174763140426 222.35018368184194 chrX 155270560 5288294 0.034058574915940276 3.260904514148198 chrY 59373566 349110 0.005879889377033544 1.0424077050150566