BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234118.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 633,067 number of mapped reads = 416,931 (65.86%) number of supplementary alignments = 1,522 (0.24%) number of secondary alignments = 0 number of mapped bases = 27,414,351 bp number of sequenced bases = 27,401,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,575 duplication rate = 1.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3762 >>>>>>> ACTG content number of A's = 7,842,195 bp (28.62%) number of C's = 4,548,049 bp (16.6%) number of T's = 8,864,289 bp (32.35%) number of G's = 6,141,889 bp (22.41%) number of N's = 4,593 bp (0.02%) GC percentage = 39.01% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 256,299 number of insertions = 2,097 mapped reads with insertion percentage = 0.5% number of deletions = 7,742 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0089X std coverageData = 0.1072X There is a 0.84% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 3178170 0.012750901029851396 0.14766617288497838 chr2 243199373 2753196 0.011320736423115697 0.1229251401815426 chr3 198022430 3988113 0.02013970336592678 0.14827892169324422 chr4 191154276 1434444 0.007504116727161259 0.08981962069722195 chr5 180915260 1292133 0.007142200165978259 0.08701112709557324 chr6 171115067 1648267 0.009632506528487055 0.11068970355872075 chr7 159138663 1203818 0.00756458535786492 0.11561540161222185 chr8 146364022 2161995 0.014771355490627334 0.15804311395410825 chr9 141213431 913244 0.006467118556166233 0.08513076332631084 chr10 135534747 1064278 0.007852436541605085 0.09895099679125222 chr11 135006516 1304424 0.009661933650669127 0.1035919384678663 chr12 133851895 692496 0.005173598774974385 0.07419265047882913 chr13 115169878 543048 0.004715191241237575 0.07091829179347153 chr14 107349540 756315 0.007045349239503029 0.08758806994919126 chr15 102531392 180607 0.0017614800353046996 0.044114497474029145 chr16 90354753 335878 0.0037173251970485715 0.0634419870254751 chr17 81195210 337943 0.004162105129107986 0.0667344435694793 chr18 78077248 550296 0.00704809677718149 0.11024757186484187 chr19 59128983 331245 0.005602075043299831 0.08492039676179226 chr20 63025520 457973 0.007266469201682112 0.08825533703837815 chr21 48129895 378242 0.007858774676321234 0.0921028513811927 chr22 51304566 73101 0.001424843940790767 0.03866186844691742 chrMT 16571 8084 0.4878402027638646 0.8920432527688452 chrX 155270560 1772067 0.011412768782440148 0.11243709822735976 chrY 59373566 54974 9.259002566899889E-4 0.032704270035203514