BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008785.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 = 1,171,058 number of mapped reads = 966,064 (82.49%) number of supplementary alignments = 6,649 (0.57%) number of secondary alignments = 0 number of mapped bases = 62,565,539 bp number of sequenced bases = 62,537,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,678 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2495 >>>>>>> ACTG content number of A's = 17,760,670 bp (28.4%) number of C's = 11,170,329 bp (17.86%) number of T's = 19,179,382 bp (30.67%) number of G's = 14,417,083 bp (23.05%) number of N's = 10,507 bp (0.02%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 493,593 number of insertions = 5,587 mapped reads with insertion percentage = 0.57% number of deletions = 16,666 mapped reads with deletion percentage = 1.71% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.1999X There is a 1.89% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 5323084 0.02135635200684214 0.28272704398460463 chr2 243199373 5417261 0.022274979302681016 0.2364066314222845 chr3 198022430 4445612 0.022450042654258914 0.15791588684440266 chr4 191154276 3865212 0.020220379480289524 0.15543781293975548 chr5 180915260 3336143 0.01844036263165418 0.1421707136561919 chr6 171115067 3714076 0.021705137163637377 0.1735899116744972 chr7 159138663 3360230 0.02111510764671939 0.2678068189526881 chr8 146364022 4234596 0.028931946130859944 0.231915486672266 chr9 141213431 2221145 0.01572899252054856 0.19522561827330306 chr10 135534747 3452781 0.025475245842307877 0.24201532894034916 chr11 135006516 2794284 0.020697401005444805 0.19921287516281394 chr12 133851895 3084226 0.023042079456551585 0.15910177597705044 chr13 115169878 1606836 0.013951877243457703 0.12174944599671439 chr14 107349540 2212793 0.020612971420278094 0.1580642824504992 chr15 102531392 1698180 0.016562537256882264 0.1337187592198848 chr16 90354753 1482010 0.016402125519617103 0.1499921687225696 chr17 81195210 1668876 0.020553872574502856 0.1670370075655514 chr18 78077248 1273780 0.01631435575188306 0.3373113321468006 chr19 59128983 1075910 0.018195983516239404 0.2228200583208242 chr20 63025520 1267310 0.020107886456153 0.15030051480667467 chr21 48129895 746966 0.015519792843927875 0.1383449982689548 chr22 51304566 657878 0.0128229912323983 0.11725756805766685 chrMT 16571 47868 2.888660913644318 2.5142126274534973 chrX 155270560 3415454 0.02199679063436108 0.1689483346036642 chrY 59373566 163028 0.002745801052272993 0.0800357062113071