BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008793.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 = 1,482,329 number of mapped reads = 1,186,009 (80.01%) number of supplementary alignments = 11,462 (0.77%) number of secondary alignments = 0 number of mapped bases = 76,627,534 bp number of sequenced bases = 76,589,861 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,696 duplication rate = 10.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1034 >>>>>>> ACTG content number of A's = 20,315,926 bp (26.53%) number of C's = 14,206,862 bp (18.55%) number of T's = 24,160,686 bp (31.55%) number of G's = 17,878,259 bp (23.34%) number of N's = 28,128 bp (0.04%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 655,612 number of insertions = 5,637 mapped reads with insertion percentage = 0.47% number of deletions = 21,967 mapped reads with deletion percentage = 1.83% homopolymer indels = 45.21% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.2979X There is a 1.43% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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% 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 7808593 0.03132827901760774 0.4133817306559911 chr2 243199373 7138112 0.02935086514388341 0.35457873031428383 chr3 198022430 3701543 0.01869254407190135 0.21349240066288092 chr4 191154276 3170351 0.01658529992810624 0.22453980401073143 chr5 180915260 2012284 0.011122798596425752 0.15957379075834088 chr6 171115067 5285201 0.030886824244413264 0.2947754407440994 chr7 159138663 6823853 0.042879919130651485 0.46290600354289657 chr8 146364022 5334646 0.03644779589344709 0.3694716270089608 chr9 141213431 3280144 0.023228272103947394 0.2619925690162104 chr10 135534747 4345269 0.03206018453703241 0.31529615352930573 chr11 135006516 4894275 0.036252139118974076 0.399550506300838 chr12 133851895 3338514 0.02494185084193242 0.24901566149974694 chr13 115169878 624389 0.005421460983053225 0.10984567413413227 chr14 107349540 3311874 0.030851310587823665 0.280122133220061 chr15 102531392 1213516 0.011835555690105134 0.1711211690460399 chr16 90354753 1915070 0.0211950111799874 0.2269202570651361 chr17 81195210 2625607 0.03233696913894305 0.32205739577173553 chr18 78077248 837673 0.010728772100164187 0.2563153122128904 chr19 59128983 1498125 0.025336559568426873 0.29854343165839126 chr20 63025520 2410173 0.0382412235551567 0.3145102509942369 chr21 48129895 1079680 0.02243262737223923 0.24845400486632158 chr22 51304566 546980 0.010661429238091597 0.15521457134695932 chrMT 16571 4316 0.2604550117675457 0.5451349390943194 chrX 155270560 3218847 0.020730568628077338 0.2348502454403573 chrY 59373566 208499 0.003511646917080911 0.11180508516398692