BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004036.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 = 2,232,348 number of mapped reads = 1,938,334 (86.83%) number of supplementary alignments = 11,955 (0.54%) number of secondary alignments = 0 number of mapped bases = 125,121,902 bp number of sequenced bases = 125,053,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,291 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9958 >>>>>>> ACTG content number of A's = 33,666,243 bp (26.92%) number of C's = 22,945,848 bp (18.35%) number of T's = 38,960,437 bp (31.15%) number of G's = 29,461,565 bp (23.56%) number of N's = 19,844 bp (0.02%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,195,625 number of insertions = 10,266 mapped reads with insertion percentage = 0.52% number of deletions = 41,087 mapped reads with deletion percentage = 2.09% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0404X std coverageData = 0.3793X There is a 3.52% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9472757 0.03800494844103117 0.6755984533587803 chr2 243199373 9081089 0.03734010037928839 0.4994374418533257 chr3 198022430 7968835 0.040242082677199746 0.22310179734245605 chr4 191154276 8658232 0.045294471989734617 0.25381734086673463 chr5 180915260 7822772 0.043239978761327263 0.23756321802930985 chr6 171115067 6855470 0.04006350884343808 0.2564337655431907 chr7 159138663 7382098 0.04638783474007193 0.5825895662355294 chr8 146364022 8562422 0.05850086573871276 0.4244274521783573 chr9 141213431 4884719 0.034591036882320354 0.3572044239082004 chr10 135534747 5284477 0.038989831884217854 0.3459277597606269 chr11 135006516 4768581 0.03532111738962288 0.2757235933739746 chr12 133851895 6167430 0.04607652360842557 0.25028186008396 chr13 115169878 3772601 0.03275683768632628 0.20882902918914512 chr14 107349540 3406735 0.031734975296587205 0.24167316153779567 chr15 102531392 3875190 0.03779515643365107 0.23199368556867955 chr16 90354753 3649723 0.04039325966615171 0.26042637166450067 chr17 81195210 3048358 0.037543569380509026 0.23332056253425934 chr18 78077248 3354339 0.042961798551096476 0.5862129559302158 chr19 59128983 2501511 0.04230600414690035 0.5138852457965036 chr20 63025520 2615754 0.04150309271545875 0.2429105503926796 chr21 48129895 1544676 0.03209389922832784 0.22147286393976717 chr22 51304566 1006767 0.019623341127181546 0.153836876609012 chrMT 16571 32549 1.9642145917566833 1.8659445147348401 chrX 155270560 9046010 0.05825965978354171 0.316602781432496 chrY 59373566 358807 0.006043211216250679 0.12482190238895376