BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013177.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,561,868 number of mapped reads = 2,293,852 (89.54%) number of supplementary alignments = 13,056 (0.51%) number of secondary alignments = 0 number of mapped bases = 148,911,282 bp number of sequenced bases = 148,848,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,211 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0255 >>>>>>> ACTG content number of A's = 40,005,701 bp (26.88%) number of C's = 28,583,281 bp (19.2%) number of T's = 45,424,702 bp (30.52%) number of G's = 34,801,872 bp (23.38%) number of N's = 33,306 bp (0.02%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,179,255 number of insertions = 10,238 mapped reads with insertion percentage = 0.44% number of deletions = 35,810 mapped reads with deletion percentage = 1.54% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.3936X There is a 4.13% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10989412 0.04408980790463106 0.6153973225817224 chr2 243199373 15101830 0.06209650055306681 0.510659332268523 chr3 198022430 9325769 0.0470945084352313 0.24441184763119364 chr4 191154276 9045927 0.047322650527577004 0.2541176292221892 chr5 180915260 7995543 0.04419496177381609 0.23769084314996886 chr6 171115067 7848289 0.04586556366775113 0.300040121459826 chr7 159138663 9383487 0.05896421914767501 0.7180772687787991 chr8 146364022 8077944 0.05519077632343282 0.36399523156859087 chr9 141213431 5343619 0.03784072777043424 0.31004037905744547 chr10 135534747 6984641 0.05153395092108742 0.4148854309358069 chr11 135006516 6279508 0.04651262906451123 0.29875984727499083 chr12 133851895 7402820 0.05530605300731827 0.27023813718911066 chr13 115169878 3692268 0.03205932023302135 0.20786997950786637 chr14 107349540 4915140 0.04578631636428065 0.2572770430448678 chr15 102531392 4216113 0.04112021613829255 0.23519364255404931 chr16 90354753 5075784 0.05617617038917698 0.30263882632278305 chr17 81195210 4069976 0.050125814072037006 0.27666269522556564 chr18 78077248 3558614 0.0455781177123456 0.5641058449783596 chr19 59128983 3268292 0.05527394239133117 0.5053580833601751 chr20 63025520 3428122 0.05439260160011373 0.2686548686829088 chr21 48129895 2516682 0.05228937233293362 0.2728219906720379 chr22 51304566 1570597 0.03061320117199705 0.1962563139362157 chrMT 16571 426051 25.710639068251766 17.91346058355374 chrX 155270560 8048496 0.05183529962151228 0.2784557730612325 chrY 59373566 346358 0.005833538783909324 0.12215659405989746