BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046415.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,898,138 number of mapped reads = 7,868,811 (99.63%) number of supplementary alignments = 35,359 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,940,441 number of mapped paired reads (second in pair) = 3,928,370 number of mapped paired reads (both in pair) = 7,848,426 number of mapped paired reads (singletons) = 20,385 number of mapped bases = 764,835,449 bp number of sequenced bases = 764,630,625 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,447,052 duplication rate = 39.9% >>>>>>> Insert size mean insert size = 15,615.4089 std insert size = 1,241,673.7454 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.4774 >>>>>>> ACTG content number of A's = 217,139,028 bp (28.4%) number of C's = 164,568,115 bp (21.52%) number of T's = 217,457,601 bp (28.44%) number of G's = 165,393,530 bp (21.63%) number of N's = 72,351 bp (0.01%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 3,057,472 number of insertions = 55,975 mapped reads with insertion percentage = 0.7% number of deletions = 71,884 mapped reads with deletion percentage = 0.89% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.2471X std coverageData = 19.2151X There is a 2.65% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 181166859 0.7268461690211797 48.78422948223313 chr2 243199373 77699668 0.319489590131468 18.894771134684046 chr3 198022430 54517975 0.27531211994520016 18.874885601080535 chr4 191154276 14584776 0.0762984553900327 4.201248049012237 chr5 180915260 39741073 0.2196667821166661 12.801352244111666 chr6 171115067 44722169 0.26135728304977374 11.776638921215984 chr7 159138663 35495582 0.22304813507199064 11.237529048206273 chr8 146364022 63738245 0.43547754515792136 21.19075962184869 chr9 141213431 13490371 0.09553178408362586 5.286829918872754 chr10 135534747 16932567 0.12493155721905026 9.428250108254373 chr11 135006516 17512928 0.12971913148251304 7.419837622245955 chr12 133851895 22924935 0.17127090356098432 8.250325631434357 chr13 115169878 14558970 0.12641300184411067 7.454145771651302 chr14 107349540 25464988 0.23721562290811865 16.045077642309224 chr15 102531392 12444817 0.12137567585154799 6.422600811012925 chr16 90354753 38414266 0.4251493665197668 26.591280203553843 chr17 81195210 33691205 0.4149407951528175 30.406133107522862 chr18 78077248 4066926 0.05208849061893165 2.2247436530835056 chr19 59128983 9309431 0.15744277218500444 9.521768884503986 chr20 63025520 17415754 0.276328604666808 17.149126872625654 chr21 48129895 5005970 0.10400957658436612 11.814039813092513 chr22 51304566 4268100 0.08319142588595331 4.186568483555254 chrMT 16571 23437 1.414338301852634 1.527152721951809 chrX 155270560 17510576 0.11277460453546377 7.218783969477668 chrY 59373566 133861 0.002254555503706818 0.10731465764275712