BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716212.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 = 1,596,767 number of mapped reads = 1,397,626 (87.53%) number of supplementary alignments = 4,599 (0.29%) number of secondary alignments = 0 number of mapped bases = 78,730,913 bp number of sequenced bases = 78,707,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,524 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0363 >>>>>>> ACTG content number of A's = 19,659,592 bp (24.98%) number of C's = 15,622,050 bp (19.85%) number of T's = 24,544,902 bp (31.18%) number of G's = 18,880,598 bp (23.99%) number of N's = 598 bp (0%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 414,658 number of insertions = 5,065 mapped reads with insertion percentage = 0.36% number of deletions = 14,786 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.63% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.2287X There is a 2.32% 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 6616194 0.02654434309313115 0.2883097747826872 chr2 243199373 6192177 0.025461319754307096 0.3637132165409835 chr3 198022430 4560558 0.023030512250556665 0.16547325798478396 chr4 191154276 4839815 0.025318894775861567 0.17954769558480982 chr5 180915260 4491788 0.024828132242686436 0.1689550606433138 chr6 171115067 4245852 0.024812847135197044 0.20653792475566637 chr7 159138663 4514000 0.028365199976576404 0.3261350475344251 chr8 146364022 4085313 0.02791200285545583 0.21695408751990278 chr9 141213431 2630487 0.01862773945348017 0.17180727962575124 chr10 135534747 3490101 0.025750599586097284 0.25638363219168275 chr11 135006516 2813816 0.02084207550397049 0.1895124889663966 chr12 133851895 3927917 0.029345247596233134 0.18535966082509361 chr13 115169878 2361691 0.020506151790835446 0.15468104506869834 chr14 107349540 2640514 0.024597348065021982 0.17489457554402008 chr15 102531392 2883923 0.028127219807958913 0.1882597415787284 chr16 90354753 2681662 0.02967925771431194 0.19532420161044092 chr17 81195210 3483465 0.04290234608667186 0.23481051781379503 chr18 78077248 1467786 0.018799151322546614 0.25448158585142144 chr19 59128983 2047374 0.034625557486757386 0.26950264620193054 chr20 63025520 2492524 0.03954785299669086 0.2224469312607871 chr21 48129895 981167 0.020385812185960514 0.16023742835669416 chr22 51304566 716100 0.013957821999702717 0.12836082298748963 chrMT 16571 23582 1.4230885281515901 1.4609690639396256 chrX 155270560 4316875 0.02780227623317646 0.1922859924636644 chrY 59373566 226232 0.003810315183022694 0.10247150375100489