BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714091.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 = 967,422 number of mapped reads = 72,708 (7.52%) number of supplementary alignments = 2,783 (0.29%) number of secondary alignments = 0 number of mapped bases = 7,379,344 bp number of sequenced bases = 7,365,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,510 duplication rate = 23.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.8024 >>>>>>> ACTG content number of A's = 191,290 bp (2.6%) number of C's = 36,591 bp (0.5%) number of T's = 57,002 bp (0.77%) number of G's = 7,078,945 bp (96.11%) number of N's = 1,315 bp (0.02%) GC percentage = 96.61% >>>>>>> Mismatches and indels general error rate = 0.0384 number of mismatches = 184,820 number of insertions = 12,310 mapped reads with insertion percentage = 10.43% number of deletions = 3,509 mapped reads with deletion percentage = 4.68% homopolymer indels = 72.58% >>>>>>> Coverage mean coverageData = 0.0024X std coverageData = 8.5628X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 12780 5.1273693717296696E-5 0.011901174136187317 chr2 243199373 7133569 0.029332184997039445 30.548726417617825 chr3 198022430 13552 6.843669174244554E-5 0.02048079559396584 chr4 191154276 13335 6.976040651060298E-5 0.027916371236537733 chr5 180915260 13803 7.629538823867042E-5 0.05168210868884273 chr6 171115067 9967 5.824735468794224E-5 0.013971140652133354 chr7 159138663 19242 1.209134200153485E-4 0.1314594747192056 chr8 146364022 8416 5.750046961677508E-5 0.03558498974991951 chr9 141213431 5621 3.980499560271997E-5 0.013261483928988575 chr10 135534747 10083 7.439420682284522E-5 0.020843142937347854 chr11 135006516 9819 7.272982290721435E-5 0.042387855096988114 chr12 133851895 17028 1.2721523292591412E-4 0.08490704127894291 chr13 115169878 3425 2.9738678719447807E-5 0.006649869351914939 chr14 107349540 15780 1.4699643799125734E-4 0.14186156550747475 chr15 102531392 6846 6.676979475710229E-5 0.024558662798069838 chr16 90354753 6738 7.457272336298678E-5 0.020453765513390752 chr17 81195210 18565 2.2864649281650973E-4 0.22276435710858775 chr18 78077248 3952 5.06165381238847E-5 0.014670821800578129 chr19 59128983 6185 1.0460183291161968E-4 0.03294201169165036 chr20 63025520 19071 3.025917120556879E-4 0.34901870453280276 chr21 48129895 3226 6.702694863556216E-5 0.03914894143635862 chr22 51304566 1573 3.066003910840996E-5 0.008824249140380061 chrMT 16571 64 0.003862168849194376 0.062026224300489936 chrX 155270560 23439 1.5095585409107817E-4 0.03436737069671253 chrY 59373566 3265 5.499080179890155E-5 0.020924907857190592