BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238060.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 = 1,483,226 number of mapped reads = 1,330,648 (89.71%) number of supplementary alignments = 15,479 (1.04%) number of secondary alignments = 0 number of mapped bases = 88,211,467 bp number of sequenced bases = 88,166,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,220 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5011 >>>>>>> ACTG content number of A's = 23,991,304 bp (27.21%) number of C's = 17,203,344 bp (19.51%) number of T's = 26,984,411 bp (30.61%) number of G's = 19,976,533 bp (22.66%) number of N's = 11,119 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 667,590 number of insertions = 6,221 mapped reads with insertion percentage = 0.46% number of deletions = 25,121 mapped reads with deletion percentage = 1.87% homopolymer indels = 44.17% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.265X There is a 2.29% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.09% 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% 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 6254806 0.02509444500039982 0.45408030273497396 chr2 243199373 8106591 0.03333310814086679 0.2864228603651912 chr3 198022430 6313001 0.03188023195150166 0.21483324776613114 chr4 191154276 5594679 0.029267872616148015 0.22601318239346652 chr5 180915260 5485704 0.030321952940840922 0.20906593234473475 chr6 171115067 4910169 0.02869512945928952 0.21989546560280646 chr7 159138663 3317505 0.020846631091779373 0.2089917393832649 chr8 146364022 5695320 0.03891202169888444 0.28213196586532 chr9 141213431 4970796 0.03520058938303114 0.271311419088385 chr10 135534747 4972416 0.03668738910177772 0.31382693374200865 chr11 135006516 5148359 0.03813415198419016 0.2888456537749939 chr12 133851895 2836599 0.0211920720285656 0.1787308821541168 chr13 115169878 2025033 0.017583008987818845 0.158764734492949 chr14 107349540 2854565 0.026591310964164356 0.22050458227570233 chr15 102531392 2742648 0.026749349116415 0.19565418598263395 chr16 90354753 2684270 0.02970812171884306 0.22650354519478177 chr17 81195210 2577610 0.031745838208928824 0.2415955876914684 chr18 78077248 1335580 0.017105879551492387 0.38431417133546586 chr19 59128983 2135382 0.036113964618671016 0.32270296090721895 chr20 63025520 1181639 0.01874857994031624 0.16873377817867333 chr21 48129895 739048 0.015355279707134205 0.1703595769025791 chr22 51304566 1409913 0.027481238219615775 0.2010680859167225 chrMT 16571 5911 0.3567075010560618 0.7394263147153152 chrX 155270560 4682384 0.030156289769290457 0.22063831428890626 chrY 59373566 231539 0.003899698394399959 0.12791681341277414