BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080654.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,512,226 number of mapped reads = 1,376,165 (91%) number of supplementary alignments = 11,953 (0.79%) number of secondary alignments = 0 number of mapped bases = 91,059,589 bp number of sequenced bases = 91,025,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,290 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.189 >>>>>>> ACTG content number of A's = 24,371,418 bp (26.77%) number of C's = 17,070,798 bp (18.75%) number of T's = 28,497,541 bp (31.31%) number of G's = 21,081,983 bp (23.16%) number of N's = 3,849 bp (0%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 620,200 number of insertions = 6,918 mapped reads with insertion percentage = 0.5% number of deletions = 21,178 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.0294X std coverageData = 0.2388X There is a 2.57% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11462349 0.045987243498181694 0.28117052643259977 chr2 243199373 6000865 0.0246746729893913 0.3611969365626875 chr3 198022430 5567041 0.028113183945879264 0.18664055704157065 chr4 191154276 3922452 0.02051982347494021 0.16259064389112696 chr5 180915260 4321218 0.023885315146992023 0.17230239098993508 chr6 171115067 5286430 0.030894006545899317 0.23765869422964406 chr7 159138663 5660752 0.035571192400931505 0.4118112440492603 chr8 146364022 10596034 0.072395072608759 0.3283310848094499 chr9 141213431 2982554 0.02112089465484342 0.1959273849789763 chr10 135534747 4448953 0.03282518393604261 0.21006631963510505 chr11 135006516 3530175 0.02614818235884259 0.19853923772621299 chr12 133851895 2850534 0.021296179631973083 0.16258142736803916 chr13 115169878 1756932 0.0152551346802677 0.13751045516577573 chr14 107349540 1704793 0.015880766699140025 0.14375737910977035 chr15 102531392 1650331 0.016095860670651968 0.15060930447234902 chr16 90354753 2378156 0.026320209187003146 0.18285783773371397 chr17 81195210 1630951 0.02008678837089035 0.1615387716194298 chr18 78077248 2780865 0.035616841925576063 0.2695672333477072 chr19 59128983 1635139 0.02765376499034323 0.2135390832388154 chr20 63025520 2370708 0.03761504863426752 0.21887039327334257 chr21 48129895 1304536 0.027104484645146223 0.18776531348374 chr22 51304566 897592 0.01749536288836358 0.14749392515804308 chrMT 16571 14945 0.9018767726751554 1.1327135439278633 chrX 155270560 6123089 0.039434964361563456 0.2288546312983629 chrY 59373566 182195 0.003068621480474998 0.06591042361444555