BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063531.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 = 4,990,100 number of mapped reads = 4,713,726 (94.46%) number of supplementary alignments = 42,749 (0.86%) number of secondary alignments = 0 number of mapped bases = 300,224,360 bp number of sequenced bases = 300,116,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 784,112 duplication rate = 13.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3833 >>>>>>> ACTG content number of A's = 78,122,569 bp (26.03%) number of C's = 54,690,122 bp (18.22%) number of T's = 97,033,456 bp (32.33%) number of G's = 70,236,381 bp (23.4%) number of N's = 34,461 bp (0.01%) GC percentage = 41.63% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,627,535 number of insertions = 18,871 mapped reads with insertion percentage = 0.4% number of deletions = 61,927 mapped reads with deletion percentage = 1.3% homopolymer indels = 43.75% >>>>>>> Coverage mean coverageData = 0.097X std coverageData = 0.9919X There is a 6.17% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 31873825 0.12787861820412474 1.916854118947354 chr2 243199373 31191302 0.12825403953652462 1.6958177990371386 chr3 198022430 18954684 0.09571988385356144 0.4516240107624308 chr4 191154276 14958360 0.07825281397314911 0.48810754564506253 chr5 180915260 15832977 0.08751598400267617 0.4382161687465569 chr6 171115067 15318210 0.08951993689719913 0.6587340594716918 chr7 159138663 28249857 0.1775172448193812 1.5137399823897284 chr8 146364022 11413041 0.07797709330507466 1.1737642305025793 chr9 141213431 10394766 0.0736103211032384 0.6821223363965269 chr10 135534747 15321016 0.11304124100368151 0.6762889221090755 chr11 135006516 14281706 0.1057853089105714 0.6690960980632022 chr12 133851895 12228031 0.09135493374972391 0.47947104519118494 chr13 115169878 7548811 0.06554501169133825 0.44017800804634566 chr14 107349540 6393634 0.05955902559060803 0.43189901223653343 chr15 102531392 4464210 0.04353993360394444 0.3639075040517487 chr16 90354753 6143333 0.0679912544279768 0.43153333553096596 chr17 81195210 7818402 0.09629141916130274 0.5025947585983327 chr18 78077248 7415920 0.09498183132684185 1.2834653481028437 chr19 59128983 5940379 0.10046475854320037 1.2805035057881105 chr20 63025520 4613904 0.0732069168171877 0.44431068227093146 chr21 48129895 5173423 0.10748876555828762 0.5147378708527321 chr22 51304566 4466898 0.08706628567913428 0.42555623966601885 chrMT 16571 448260 27.05087200531048 17.79326320391048 chrX 155270560 18982112 0.12225184220369914 0.6427126366162913 chrY 59373566 797299 0.013428518004123249 0.4589688247950581