BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524416.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 = 1,401,525 number of mapped reads = 1,297,324 (92.57%) number of supplementary alignments = 5,261 (0.38%) number of secondary alignments = 0 number of mapped bases = 76,555,726 bp number of sequenced bases = 76,533,495 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,361 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2045 >>>>>>> ACTG content number of A's = 20,016,355 bp (26.15%) number of C's = 13,706,312 bp (17.91%) number of T's = 23,850,714 bp (31.16%) number of G's = 18,949,891 bp (24.76%) number of N's = 10,223 bp (0.01%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 368,690 number of insertions = 5,751 mapped reads with insertion percentage = 0.44% number of deletions = 13,920 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.46% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2586X There is a 2.25% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 6129859 0.024593154373725713 0.5164402521806626 chr2 243199373 6551472 0.026938687872357304 0.28435365836970855 chr3 198022430 5093039 0.02571950561358125 0.17156240833289216 chr4 191154276 5002536 0.026170149602094173 0.19434434192098035 chr5 180915260 4648587 0.02569483082853265 0.172502488671504 chr6 171115067 4449086 0.026000550845706648 0.18862045268351726 chr7 159138663 4283974 0.026919756137451022 0.35515924881650907 chr8 146364022 3856741 0.026350334920421905 0.22902659934116254 chr9 141213431 3204600 0.02269330882556065 0.21259898593896992 chr10 135534747 3697323 0.02727952116957875 0.23497929897051334 chr11 135006516 3520245 0.026074630353397164 0.2341217662794198 chr12 133851895 3375888 0.02522106989968278 0.1735452523145253 chr13 115169878 2328949 0.02022185870510343 0.15290874143737146 chr14 107349540 2270240 0.02114811111440254 0.16368350716881816 chr15 102531392 2238820 0.021835458939248577 0.15779339713818227 chr16 90354753 2168731 0.024002400847689773 0.17578696783574552 chr17 81195210 2042571 0.025156299244746088 0.1804891244386827 chr18 78077248 2085319 0.026708408062743196 0.38537370454083 chr19 59128983 1550111 0.02621575615464247 0.3426607464847601 chr20 63025520 1664112 0.02640378056380971 0.17842344319535564 chr21 48129895 974757 0.020252630927202312 0.16935470117151336 chr22 51304566 879565 0.017143990653775337 0.14016363695906958 chrMT 16571 2197 0.1325810150262507 0.45076087265000586 chrX 155270560 4316091 0.02779722698237193 0.1984780726730965 chrY 59373566 220913 0.003720729861500992 0.10506729379716323