BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716915.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 = 660,021 number of mapped reads = 533,276 (80.8%) number of supplementary alignments = 2,410 (0.37%) number of secondary alignments = 0 number of mapped bases = 29,283,179 bp number of sequenced bases = 29,274,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,901 duplication rate = 1.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.202 >>>>>>> ACTG content number of A's = 7,081,103 bp (24.19%) number of C's = 6,105,693 bp (20.86%) number of T's = 8,796,428 bp (30.05%) number of G's = 7,290,767 bp (24.9%) number of N's = 733 bp (0%) GC percentage = 45.76% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 158,635 number of insertions = 2,232 mapped reads with insertion percentage = 0.42% number of deletions = 4,973 mapped reads with deletion percentage = 0.92% homopolymer indels = 32.94% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.113X There is a 0.89% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% 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 2791985 0.011201516725609281 0.13208938282088073 chr2 243199373 2547185 0.010473649535272444 0.1291616306762534 chr3 198022430 2005032 0.010125277222383343 0.10691876624440691 chr4 191154276 1886023 0.009866496525560329 0.11449708160444133 chr5 180915260 1806489 0.009985277084973375 0.10450965395097093 chr6 171115067 1260302 0.007365231023168755 0.09096431788713262 chr7 159138663 1688708 0.010611550758095787 0.12249986095596503 chr8 146364022 1790978 0.012236463411752925 0.11932649010064655 chr9 141213431 1299839 0.009204783077609665 0.10512607452323257 chr10 135534747 1565520 0.01155069113014982 0.1693713194373471 chr11 135006516 1220415 0.009039674796140951 0.10867971501786396 chr12 133851895 1424143 0.010639692475029957 0.10825159267210305 chr13 115169878 559898 0.004861496857711354 0.07429675145921477 chr14 107349540 937168 0.008730060697046304 0.09974631614164398 chr15 102531392 571587 0.005574751194248879 0.07930324317681936 chr16 90354753 783276 0.008668896477421613 0.10342238640703617 chr17 81195210 1118817 0.013779347328493886 0.12763906698077113 chr18 78077248 776792 0.009949018694921215 0.12046813782893245 chr19 59128983 751499 0.01270948631063044 0.12857938867068583 chr20 63025520 737285 0.011698197809395305 0.11734302484354084 chr21 48129895 398093 0.008271221036322643 0.10288071049321765 chr22 51304566 324693 0.006328734951193233 0.08566068785995047 chrMT 16571 4186 0.25260998129261963 0.5412541406730048 chrX 155270560 933632 0.0060129363866530785 0.08423205266433723 chrY 59373566 99634 0.0016780868442363727 0.0675038781607595