BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716867.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,854,240 number of mapped reads = 1,559,069 (84.08%) number of supplementary alignments = 5,407 (0.29%) number of secondary alignments = 0 number of mapped bases = 89,031,498 bp number of sequenced bases = 89,003,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,039 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3429 >>>>>>> ACTG content number of A's = 21,838,517 bp (24.54%) number of C's = 17,729,291 bp (19.92%) number of T's = 27,548,313 bp (30.95%) number of G's = 21,885,959 bp (24.59%) number of N's = 1,317 bp (0%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 466,832 number of insertions = 7,539 mapped reads with insertion percentage = 0.48% number of deletions = 17,520 mapped reads with deletion percentage = 1.11% homopolymer indels = 38.98% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.2438X There is a 2.59% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7130361 0.0286071945232987 0.3125447241247764 chr2 243199373 7501476 0.03084496439059487 0.37861429242528605 chr3 198022430 5912770 0.029859092225057535 0.1898580335536577 chr4 191154276 5701079 0.029824491082794297 0.21317170421362655 chr5 180915260 5243588 0.028983668928757034 0.18511697225800905 chr6 171115067 5121602 0.02993074829582365 0.21221766479618473 chr7 159138663 4947450 0.031088925260104767 0.3152386601105842 chr8 146364022 4481016 0.030615556601744656 0.2266528719878415 chr9 141213431 3679441 0.026055885576493073 0.2074496253265805 chr10 135534747 4287868 0.03163666952504807 0.28095950886460025 chr11 135006516 3971218 0.029415009865153472 0.22016296869037913 chr12 133851895 4038574 0.03017195983665379 0.19163266627993253 chr13 115169878 2762873 0.023989545252448737 0.16895040293217423 chr14 107349540 2696014 0.025114350746169942 0.17844050269330025 chr15 102531392 2599485 0.025353064552171494 0.1782199767267025 chr16 90354753 2679837 0.029659059551632 0.2018540405941169 chr17 81195210 2557479 0.03149790486409235 0.20459090059780707 chr18 78077248 2329908 0.029841062021038447 0.3268359981429778 chr19 59128983 1999133 0.03380969701440662 0.2840708204987794 chr20 63025520 1914382 0.030374711704084314 0.19494667321143025 chr21 48129895 1143596 0.023760616972050324 0.18893600371335312 chr22 51304566 1127667 0.021979856529728756 0.16396094365222658 chrMT 16571 7518 0.45368414700380183 0.7408526347697774 chrX 155270560 4916036 0.03166109531645922 0.21156386725903198 chrY 59373566 281127 0.004734884881261806 0.12314173515435442