BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524876.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 = 2,026,831 number of mapped reads = 1,856,584 (91.6%) number of supplementary alignments = 9,046 (0.45%) number of secondary alignments = 0 number of mapped bases = 107,949,742 bp number of sequenced bases = 107,918,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,332 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4032 >>>>>>> ACTG content number of A's = 28,370,029 bp (26.29%) number of C's = 19,431,952 bp (18.01%) number of T's = 35,313,542 bp (32.72%) number of G's = 24,788,159 bp (22.97%) number of N's = 14,388 bp (0.01%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 521,422 number of insertions = 7,933 mapped reads with insertion percentage = 0.42% number of deletions = 20,560 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.51% >>>>>>> Coverage mean coverageData = 0.0349X std coverageData = 0.3368X There is a 3.13% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8869010 0.03558269971170904 0.6686305108273709 chr2 243199373 7380276 0.030346607842611503 0.3851508707679908 chr3 198022430 7772895 0.039252598809134905 0.2129862159765823 chr4 191154276 5866710 0.030690969214834617 0.2046690754014944 chr5 180915260 6526845 0.036076807451179076 0.20794101066196324 chr6 171115067 7220840 0.04219873870019874 0.25004126010322475 chr7 159138663 4877984 0.03065241285833852 0.4329002451786729 chr8 146364022 11587011 0.07916570508017333 0.4606690295989364 chr9 141213431 4388360 0.031076080858059456 0.2754347297072568 chr10 135534747 5301590 0.03911609470890885 0.29557228828073456 chr11 135006516 5142619 0.038091635517799746 0.30130044090955177 chr12 133851895 4217912 0.03151178397586377 0.1970850818693422 chr13 115169878 2819720 0.02448313785658434 0.1687472734639368 chr14 107349540 2257333 0.02102787771610386 0.17036621637922897 chr15 102531392 3172723 0.030943918131921978 0.19065346955935425 chr16 90354753 3009700 0.033309813817984764 0.21444706476234168 chr17 81195210 3279916 0.040395437119997595 0.24681993907152328 chr18 78077248 2560047 0.03278864285790401 0.516098502830403 chr19 59128983 1531267 0.02589706303590576 0.4456017047260804 chr20 63025520 2217566 0.03518520751593957 0.20441547047930436 chr21 48129895 1532817 0.03184750351107145 0.20806362621837382 chr22 51304566 627065 0.012222401413550599 0.12180177605205963 chrMT 16571 24634 1.4865729286102227 1.4486933276332725 chrX 155270560 5505484 0.035457359076955734 0.2372556534123944 chrY 59373566 259418 0.004369250787463229 0.11547109686715172