BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525167.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 = 1,183,570 number of mapped reads = 1,075,711 (90.89%) number of supplementary alignments = 3,196 (0.27%) number of secondary alignments = 0 number of mapped bases = 64,100,715 bp number of sequenced bases = 64,079,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,689 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.049 >>>>>>> ACTG content number of A's = 15,642,471 bp (24.41%) number of C's = 11,701,472 bp (18.26%) number of T's = 20,685,175 bp (32.28%) number of G's = 16,049,138 bp (25.05%) number of N's = 1,547 bp (0%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 324,595 number of insertions = 4,716 mapped reads with insertion percentage = 0.44% number of deletions = 12,711 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2136X There is a 1.92% of reference with a coverageData >= 1X There is a 0.11% 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 6996782 0.0280712720872218 0.39520092621210523 chr2 243199373 5389015 0.02215883591114357 0.26593712899672123 chr3 198022430 5067487 0.02559046972608103 0.17095801745996556 chr4 191154276 3635659 0.019019501295383004 0.15121535268023628 chr5 180915260 2907904 0.016073293098658455 0.13347293026364382 chr6 171115067 3217121 0.0188009218381687 0.16237785490359827 chr7 159138663 3828679 0.024058760629401543 0.28486793408220684 chr8 146364022 3007971 0.020551300510175924 0.18412800837169802 chr9 141213431 2176447 0.015412464555159771 0.1548880563879734 chr10 135534747 3605880 0.026604838093658743 0.24192648016748336 chr11 135006516 3009708 0.0222930573217666 0.18373088108105692 chr12 133851895 2966397 0.02216178560639728 0.15864847210345176 chr13 115169878 2045255 0.01775859309323919 0.14118902045722223 chr14 107349540 2468509 0.022995058944826407 0.16305491954563942 chr15 102531392 1818042 0.017731564592432334 0.1422990508464531 chr16 90354753 1815382 0.020091715595747354 0.1640858342952065 chr17 81195210 1334412 0.016434614800552888 0.1393797080069159 chr18 78077248 1427076 0.01827774462542532 0.28930567831486065 chr19 59128983 1211667 0.02049193032797469 0.26878348777339406 chr20 63025520 1237285 0.019631492132076024 0.1501671381232288 chr21 48129895 844954 0.017555700048795038 0.1450927768376149 chr22 51304566 540133 0.010527971331050729 0.10770383847555301 chrMT 16571 65721 3.9660249834047434 2.8222442950134807 chrX 155270560 3295377 0.0212234502149023 0.16327620437919468 chrY 59373566 187852 0.003163899571065009 0.0904267317159339