BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472763.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 = 19,712,950 number of mapped reads = 19,487,867 (98.86%) number of supplementary alignments = 60,785 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,789,590 number of mapped paired reads (second in pair) = 9,698,277 number of mapped paired reads (both in pair) = 19,351,250 number of mapped paired reads (singletons) = 136,617 number of mapped bases = 1,918,593,164 bp number of sequenced bases = 1,918,322,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,531,258 duplication rate = 48.3% >>>>>>> Insert size mean insert size = 21,045.4065 std insert size = 1,417,839.7177 median insert size = 246 >>>>>>> Mapping quality mean mapping quality = 55.2158 >>>>>>> ACTG content number of A's = 527,796,463 bp (27.51%) number of C's = 434,623,053 bp (22.66%) number of T's = 524,559,256 bp (27.34%) number of G's = 430,973,684 bp (22.47%) number of N's = 369,737 bp (0.02%) GC percentage = 45.12% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 12,184,887 number of insertions = 106,755 mapped reads with insertion percentage = 0.54% number of deletions = 101,809 mapped reads with deletion percentage = 0.52% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.6198X std coverageData = 19.8978X There is a 5.38% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 215418750 0.8642656501144685 29.965852243800768 chr2 243199373 120649792 0.49609417372963377 16.304311102507434 chr3 198022430 202026855 1.0202220778726936 22.024589974244233 chr4 191154276 75886994 0.3969934420928151 13.025139891052781 chr5 180915260 103290797 0.5709346851116927 20.437887824529035 chr6 171115067 143839092 0.8405986364719128 22.372287367387354 chr7 159138663 60028201 0.37720689534761265 12.706322831776578 chr8 146364022 98538011 0.6732392951049131 21.733635625464732 chr9 141213431 111526649 0.7897736653675669 20.151413933445873 chr10 135534747 43352507 0.31986267698570314 13.054451094683678 chr11 135006516 72034753 0.5335650095585016 17.15832370455201 chr12 133851895 110372458 0.8245864430981721 25.65320465391387 chr13 115169878 43001089 0.37337096944741055 11.633726927138513 chr14 107349540 36021088 0.3355495328624603 15.510415632691853 chr15 102531392 42141738 0.4110130290633331 13.001045625706828 chr16 90354753 68826132 0.7617322798724269 19.187429733433216 chr17 81195210 89575221 1.103208194177957 26.609651226916025 chr18 78077248 23262948 0.29794784775201094 10.807812662771717 chr19 59128983 48199809 0.8151638427469655 19.49105140559551 chr20 63025520 46153665 0.7323012170308154 23.453458956614487 chr21 48129895 7385080 0.15344060069110893 6.124964885688053 chr22 51304566 35558015 0.6930770060504946 19.82868866176803 chrMT 16571 2141 0.1292016172832056 0.4631349215386901 chrX 155270560 118815571 0.7652163488043064 26.16699165078066 chrY 59373566 2685808 0.04523575356750511 1.594230601347633