BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231725.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 = 1,612,960 number of mapped reads = 1,223,625 (75.86%) number of supplementary alignments = 6,542 (0.41%) number of secondary alignments = 0 number of mapped bases = 77,149,988 bp number of sequenced bases = 77,102,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,010 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9965 >>>>>>> ACTG content number of A's = 20,163,326 bp (26.15%) number of C's = 14,562,907 bp (18.89%) number of T's = 23,702,085 bp (30.74%) number of G's = 18,661,955 bp (24.2%) number of N's = 12,455 bp (0.02%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 669,061 number of insertions = 6,347 mapped reads with insertion percentage = 0.51% number of deletions = 26,669 mapped reads with deletion percentage = 2.15% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2488X There is a 2.2% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 6750102 0.027081585485799052 0.40210319888132523 chr2 243199373 5408527 0.022239066381145645 0.2908787129117408 chr3 198022430 6749077 0.034082386525607224 0.20515413045812148 chr4 191154276 3216730 0.01682792594187116 0.1565878116156905 chr5 180915260 4165725 0.02302583541045681 0.17033305972820542 chr6 171115067 5353700 0.03128713382089258 0.24272081343340335 chr7 159138663 4677057 0.029389822132664268 0.3720103419486665 chr8 146364022 3462222 0.023654870593813007 0.2836907161637424 chr9 141213431 3476199 0.024616631544063256 0.2189758015762697 chr10 135534747 3825153 0.02822267414569343 0.22253822082473718 chr11 135006516 3594102 0.026621692837403493 0.24059690513101545 chr12 133851895 2907157 0.021719206889076918 0.16596799813659197 chr13 115169878 3056168 0.026536174675812367 0.18625092851490044 chr14 107349540 3368051 0.031374619770145266 0.2072465856243338 chr15 102531392 1554797 0.01516410700831995 0.14713061393655774 chr16 90354753 2166006 0.02397224194724986 0.1841398803282801 chr17 81195210 2189713 0.026968499742780393 0.20189086622058144 chr18 78077248 1518755 0.01945195353196875 0.36153441136684356 chr19 59128983 2616287 0.044247116511373114 0.32202275962575705 chr20 63025520 1885014 0.02990874172874734 0.20033852490868775 chr21 48129895 1259677 0.02617244438202078 0.18515797914382018 chr22 51304566 786128 0.015322768737581758 0.1368816776693472 chrMT 16571 42625 2.5722647999517227 2.627832529188981 chrX 155270560 2877572 0.01853263104093912 0.16433978499394003 chrY 59373566 243444 0.004100208500193504 0.08590364586453983