BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714260.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 246,400 number of mapped reads = 199,126 (80.81%) number of supplementary alignments = 5,991 (2.43%) number of secondary alignments = 0 number of mapped bases = 25,757,679 bp number of sequenced bases = 25,201,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,124 duplication rate = 42.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.1351 >>>>>>> ACTG content number of A's = 6,716,440 bp (26.65%) number of C's = 5,512,382 bp (21.87%) number of T's = 6,357,334 bp (25.23%) number of G's = 6,615,127 bp (26.25%) number of N's = 141 bp (0%) GC percentage = 48.12% >>>>>>> Mismatches and indels general error rate = 0.0437 number of mismatches = 1,019,621 number of insertions = 27,026 mapped reads with insertion percentage = 13.05% number of deletions = 88,795 mapped reads with deletion percentage = 42.39% homopolymer indels = 29.19% >>>>>>> Coverage mean coverageData = 0.0083X std coverageData = 2.1993X There is a 0.04% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 2101686 0.00843201911220113 1.7282005594566605 chr2 243199373 3255422 0.013385815760306258 4.8166369278084264 chr3 198022430 940098 0.004747431894457613 0.9215595843589292 chr4 191154276 1010269 0.005285097572183005 1.3261930334115144 chr5 180915260 1377469 0.007613890613760277 1.5886058822246847 chr6 171115067 1022230 0.005973933318215631 1.0754851785253854 chr7 159138663 766319 0.004815416854419595 0.7795203108946549 chr8 146364022 874482 0.005974705997078981 1.3859108131291216 chr9 141213431 990766 0.007016089000769339 1.1002027097673168 chr10 135534747 1250186 0.009224099558764808 1.6268802125330635 chr11 135006516 1253479 0.009284581493829528 1.6079422490471103 chr12 133851895 1844334 0.013778915868169069 4.6225677838466765 chr13 115169878 722307 0.006271665929871003 1.4926219831152514 chr14 107349540 1286362 0.011982929782465766 3.7220892901374234 chr15 102531392 954006 0.00930452597385979 1.7338230747556127 chr16 90354753 475700 0.005264803280464947 0.7016000091853394 chr17 81195210 750100 0.00923822969359892 1.6491683167342914 chr18 78077248 826520 0.0105859263892088 2.0867180286924887 chr19 59128983 574460 0.009715370886727411 1.1197023779914965 chr20 63025520 630574 0.010005058268460142 1.3340580467454632 chr21 48129895 265757 0.005521661744743054 1.1769383278441736 chr22 51304566 187497 0.0036545870010868038 0.5942385309540387 chrMT 16571 30382 1.8334439683784924 14.71427286537948 chrX 155270560 2140552 0.013785948862424404 1.5061102530149886 chrY 59373566 226722 0.0038185680139205384 0.6710535066509644