BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174065.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,554,330 number of mapped reads = 2,485,569 (97.31%) number of supplementary alignments = 247,690 (9.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,243,518 number of mapped paired reads (second in pair) = 1,242,051 number of mapped paired reads (both in pair) = 2,440,572 number of mapped paired reads (singletons) = 44,997 number of mapped bases = 293,394,490 bp number of sequenced bases = 293,221,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,938,411 duplication rate = 64.81% >>>>>>> Insert size mean insert size = 819,116.1752 std insert size = 8,536,957.5746 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.9167 >>>>>>> ACTG content number of A's = 88,595,884 bp (30.21%) number of C's = 57,183,835 bp (19.5%) number of T's = 88,255,729 bp (30.1%) number of G's = 59,182,296 bp (20.18%) number of N's = 3,522 bp (0%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 3,067,295 number of insertions = 34,290 mapped reads with insertion percentage = 1.33% number of deletions = 67,544 mapped reads with deletion percentage = 2.65% homopolymer indels = 42.83% >>>>>>> Coverage mean coverageData = 0.0948X std coverageData = 1.5821X There is a 1.97% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.99% of reference with a coverageData >= 4X There is a 0.76% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 24729899 0.09921700054661048 1.1721372835739088 chr2 243199373 25970918 0.10678858945906904 4.303369607893518 chr3 198022430 21611136 0.10913478841765552 0.9595640998894827 chr4 191154276 19741649 0.10327599995722826 1.1697701547774344 chr5 180915260 18832512 0.10409576284499163 0.9455479292461131 chr6 171115067 17213694 0.10059718470028124 1.0112831956422836 chr7 159138663 15658150 0.0983931227322175 1.1905217084091304 chr8 146364022 14627985 0.09994249133164707 1.3130636198864534 chr9 141213431 12633935 0.0894669502081569 1.1488342304683308 chr10 135534747 14705484 0.10849973402023616 1.4856570749656963 chr11 135006516 11381803 0.08430558270239341 0.8549761703920831 chr12 133851895 13833521 0.10334945949028215 0.935413390847374 chr13 115169878 10094740 0.08765086996098059 0.8795901642421599 chr14 107349540 8918474 0.08307882828375418 0.8355382428341832 chr15 102531392 9136277 0.08910711950540962 0.8630229710900844 chr16 90354753 9135175 0.10110342507383092 1.080267387037847 chr17 81195210 7743508 0.09536902484764803 0.940518293870275 chr18 78077248 8660070 0.11091669112108049 1.5556796949896061 chr19 59128983 5063944 0.08564233211993516 1.0046575204275467 chr20 63025520 6453529 0.10239548995391073 0.9592581762845609 chr21 48129895 4383107 0.09106828510637723 1.2648803842323784 chr22 51304566 3411837 0.0665016248261412 0.8270189156953865 chrMT 16571 321054 19.374449339207047 19.586326976521978 chrX 155270560 6559119 0.042243159295619205 0.5951142839521201 chrY 59373566 2572970 0.04333527819433988 0.7982920830048751