BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472621.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 21,710,078 number of mapped reads = 21,530,162 (99.17%) number of supplementary alignments = 129,998 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,798,334 number of mapped paired reads (second in pair) = 10,731,828 number of mapped paired reads (both in pair) = 21,401,164 number of mapped paired reads (singletons) = 128,998 number of mapped bases = 2,118,971,639 bp number of sequenced bases = 2,118,659,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,127,474 duplication rate = 50.07% >>>>>>> Insert size mean insert size = 25,380.8722 std insert size = 1,629,712.5626 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 54.7245 >>>>>>> ACTG content number of A's = 558,358,553 bp (26.35%) number of C's = 504,470,671 bp (23.81%) number of T's = 558,081,514 bp (26.34%) number of G's = 497,352,395 bp (23.47%) number of N's = 396,658 bp (0.02%) GC percentage = 47.29% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 13,308,534 number of insertions = 121,032 mapped reads with insertion percentage = 0.56% number of deletions = 108,785 mapped reads with deletion percentage = 0.5% homopolymer indels = 47.49% >>>>>>> Coverage mean coverageData = 0.6845X std coverageData = 35.3111X There is a 3.64% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 247654773 0.9935974161524757 39.224557952240026 chr2 243199373 159282978 0.6549481441302893 28.938132944529215 chr3 198022430 167518432 0.8459568544836057 58.62741237550365 chr4 191154276 41044995 0.21472182500379955 21.34367292292331 chr5 180915260 43724492 0.24168493028172416 12.13346759604251 chr6 171115067 225736509 1.3192088397452457 48.319111378466594 chr7 159138663 110645719 0.6952786765589454 31.77723026277945 chr8 146364022 103480351 0.7070067465076902 28.560872540631095 chr9 141213431 98441060 0.6971083366708936 25.94946094243752 chr10 135534747 45198706 0.3334842687978751 16.51850546940105 chr11 135006516 55758309 0.41300457675687297 24.33607975460142 chr12 133851895 104285077 0.7791079610789223 38.635071695316334 chr13 115169878 83475158 0.7248002641801878 37.10398752378146 chr14 107349540 45436068 0.42325349507785504 23.876229037905947 chr15 102531392 24891860 0.2427730621271581 18.669585033735384 chr16 90354753 126858570 1.4040054981944337 63.55420084959125 chr17 81195210 78974620 0.9726512192036944 29.385725443761284 chr18 78077248 19360238 0.2479626074935428 12.968474943386244 chr19 59128983 76985475 1.3019922057512812 61.15268383474617 chr20 63025520 131820266 2.091537935744124 67.44908120880947 chr21 48129895 16203466 0.3366611541537749 26.185221120323504 chr22 51304566 18897286 0.3683353641467311 11.902265254526444 chrMT 16571 4384 0.2645585661698147 0.6671772892773491 chrX 155270560 92304232 0.5944734919485058 29.45182193033969 chrY 59373566 988615 0.016650760036882407 0.8935678068936203