BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926894.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 30,430,458 number of mapped reads = 29,489,802 (96.91%) number of supplementary alignments = 906,077 (2.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,744,127 number of mapped paired reads (second in pair) = 14,745,675 number of mapped paired reads (both in pair) = 29,121,330 number of mapped paired reads (singletons) = 368,472 number of mapped bases = 2,686,383,818 bp number of sequenced bases = 2,684,255,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,885,356 duplication rate = 7.76% >>>>>>> Insert size mean insert size = 288,974.5664 std insert size = 5,340,069.5677 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.5473 >>>>>>> ACTG content number of A's = 745,828,134 bp (27.79%) number of C's = 543,316,279 bp (20.24%) number of T's = 754,705,522 bp (28.12%) number of G's = 640,098,064 bp (23.85%) number of N's = 307,500 bp (0.01%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 25,962,082 number of insertions = 455,930 mapped reads with insertion percentage = 1.52% number of deletions = 1,433,626 mapped reads with deletion percentage = 4.74% homopolymer indels = 51.86% >>>>>>> Coverage mean coverageData = 0.8678X std coverageData = 3.0103X There is a 32.56% of reference with a coverageData >= 1X There is a 18.5% of reference with a coverageData >= 2X There is a 10.93% of reference with a coverageData >= 3X There is a 7% of reference with a coverageData >= 4X There is a 4.66% of reference with a coverageData >= 5X There is a 3.2% of reference with a coverageData >= 6X There is a 2.26% of reference with a coverageData >= 7X There is a 1.62% of reference with a coverageData >= 8X There is a 1.19% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 225129281 0.9032245540523648 2.649741440726129 chr2 243199373 230406815 0.9473988857693313 5.360418958164723 chr3 198022430 176787798 0.8927665315489766 1.9651978729328516 chr4 191154276 138714341 0.7256669529066668 2.1854974725284286 chr5 180915260 152514716 0.8430174215265203 1.8750974821550124 chr6 171115067 144108636 0.8421738571975079 2.0152552329092686 chr7 159138663 137571645 0.8644765665776644 1.9802808568240107 chr8 146364022 129710039 0.8862153227792552 2.078916830613993 chr9 141213431 118892375 0.8419339021654392 3.0140577098214907 chr10 135534747 137564209 1.0149737395385405 6.718024177118819 chr11 135006516 135705259 1.005175624263943 2.2576438036699162 chr12 133851895 121334802 0.9064855002613149 2.0492389094096293 chr13 115169878 72673296 0.6310095770006807 1.6127766818396234 chr14 107349540 84430259 0.7864985634777755 1.8731350968982066 chr15 102531392 89374492 0.8716792999357699 2.0216404290560326 chr16 90354753 94485949 1.0457219555456037 4.498842199277577 chr17 81195210 82728329 1.0188818897075334 2.2645553884113094 chr18 78077248 70441859 0.9022072473660957 2.557980919824053 chr19 59128983 57014659 0.9642421720664467 2.274343265566672 chr20 63025520 70924266 1.125326153596194 2.400418448812116 chr21 48129895 35079374 0.7288479228969853 3.1419182660267992 chr22 51304566 43407877 0.8460821401354414 2.1915387565959263 chrMT 16571 1798335 108.5230221471245 67.95958468621772 chrX 155270560 131448451 0.8465767818445429 1.9211264842965103 chrY 59373566 4136756 0.0696733627217203 2.051063360856492