BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156413.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 = 1,695,956 number of mapped reads = 1,666,355 (98.25%) number of supplementary alignments = 210,060 (12.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 832,965 number of mapped paired reads (second in pair) = 833,390 number of mapped paired reads (both in pair) = 1,648,600 number of mapped paired reads (singletons) = 17,755 number of mapped bases = 187,343,791 bp number of sequenced bases = 187,227,558 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,250,157 duplication rate = 60.79% >>>>>>> Insert size mean insert size = 935,389.7862 std insert size = 9,087,271.003 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 52.7113 >>>>>>> ACTG content number of A's = 56,506,086 bp (30.18%) number of C's = 36,709,935 bp (19.61%) number of T's = 56,034,602 bp (29.93%) number of G's = 37,975,301 bp (20.28%) number of N's = 1,634 bp (0%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,485,820 number of insertions = 20,213 mapped reads with insertion percentage = 1.17% number of deletions = 49,625 mapped reads with deletion percentage = 2.91% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 1.2309X There is a 1.53% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 14855262 0.059599699051502066 0.7678611101883869 chr2 243199373 17533189 0.07209389063679864 3.5836327300916375 chr3 198022430 12314944 0.06218964185016818 0.7063205547067227 chr4 191154276 13258326 0.06935929594376429 0.8276056315898305 chr5 180915260 11845527 0.06547555468786878 0.7234604017743116 chr6 171115067 12134300 0.07091310083173447 0.793150241958615 chr7 159138663 10153993 0.06380594639028732 0.7755337209571791 chr8 146364022 9545298 0.06521614990875285 0.9330726132507934 chr9 141213431 7833547 0.05547310156354745 0.7080525920495808 chr10 135534747 9303192 0.06864064165036586 0.9189353904682049 chr11 135006516 8270614 0.06126085055035418 0.6999660150077781 chr12 133851895 8292872 0.06195558157768331 0.7078815790315134 chr13 115169878 6231381 0.05410599636130552 0.66508433104957 chr14 107349540 5656980 0.05269682571532212 0.6500630383133725 chr15 102531392 5309960 0.05178862684318184 0.6396946230412665 chr16 90354753 5604763 0.06203063827754584 0.7532291677714338 chr17 81195210 4992382 0.06148616402371519 0.7085963144639498 chr18 78077248 5237339 0.06707893956508303 0.8278044902630302 chr19 59128983 3208441 0.05426173150990945 0.6391665520962684 chr20 63025520 4106780 0.06516058891699743 0.7208765096145555 chr21 48129895 2663359 0.05533689612246193 0.7211372001636119 chr22 51304566 2205559 0.04298952650725084 0.6324928609404155 chrMT 16571 189250 11.420553979844307 13.082272091781995 chrX 155270560 5255804 0.033849327264614745 0.5180052542066285 chrY 59373566 1340729 0.022581244320073347 0.4751435084120289