BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524364.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 = 2,655,216 number of mapped reads = 2,439,644 (91.88%) number of supplementary alignments = 11,332 (0.43%) number of secondary alignments = 0 number of mapped bases = 143,096,485 bp number of sequenced bases = 143,054,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,304 duplication rate = 4.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1069 >>>>>>> ACTG content number of A's = 35,289,856 bp (24.67%) number of C's = 27,321,355 bp (19.1%) number of T's = 45,558,498 bp (31.85%) number of G's = 34,864,694 bp (24.37%) number of N's = 20,534 bp (0.01%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 745,123 number of insertions = 9,971 mapped reads with insertion percentage = 0.41% number of deletions = 26,024 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.94% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.4551X There is a 3.86% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 11542708 0.046309645904553234 0.9394580197095762 chr2 243199373 11779027 0.04843362404556857 0.592014094698168 chr3 198022430 9287598 0.046901747443458805 0.25180311734559285 chr4 191154276 8943276 0.0467856444916775 0.3201310451144092 chr5 180915260 8539656 0.04720251901359786 0.2569748686171166 chr6 171115067 8342178 0.04875186122563947 0.2952289493841372 chr7 159138663 7676287 0.04823646784062777 0.5683832419790301 chr8 146364022 7584682 0.0518206721594464 0.39379209053825115 chr9 141213431 6072834 0.043004648757525056 0.3740814982727921 chr10 135534747 7155582 0.05279518469164221 0.4402879164186858 chr11 135006516 6402577 0.0474242072878912 0.3733693486617852 chr12 133851895 6555041 0.0489723436489263 0.2685103190353713 chr13 115169878 4267669 0.03705542694071448 0.2232435679704317 chr14 107349540 4411858 0.04109806152872197 0.25800499945081146 chr15 102531392 4139406 0.04037208428809783 0.23313877981429845 chr16 90354753 4416834 0.048883250225917836 0.29124435338197396 chr17 81195210 3971501 0.0489129962223141 0.28755348596549507 chr18 78077248 3779425 0.048406227125218346 0.7390387992800809 chr19 59128983 3036613 0.0513557454556592 0.5934611346739306 chr20 63025520 3042587 0.048275476346724314 0.26793454631904184 chr21 48129895 1890915 0.03928774413490825 0.28735637981864415 chr22 51304566 1740738 0.03392949469643696 0.21772579951934315 chrMT 16571 146182 8.821555729889566 5.891372311681299 chrX 155270560 7876896 0.05073013197092868 0.31413025389599125 chrY 59373566 494415 0.008327190588485118 0.24816867580683022