BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524949.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 = 1,678,464 number of mapped reads = 1,529,909 (91.15%) number of supplementary alignments = 4,026 (0.24%) number of secondary alignments = 0 number of mapped bases = 89,362,129 bp number of sequenced bases = 89,332,682 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,466 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4845 >>>>>>> ACTG content number of A's = 23,846,061 bp (26.69%) number of C's = 15,767,205 bp (17.65%) number of T's = 27,714,643 bp (31.02%) number of G's = 22,003,725 bp (24.63%) number of N's = 1,048 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 436,888 number of insertions = 6,357 mapped reads with insertion percentage = 0.41% number of deletions = 17,214 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2694X There is a 2.62% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 9377472 0.037622662532904985 0.5023595762845274 chr2 243199373 8372633 0.03442703365851194 0.3176536557736962 chr3 198022430 4868733 0.024586775346610988 0.16952108296296078 chr4 191154276 5636176 0.029484959049516632 0.20111118873720793 chr5 180915260 3748898 0.02072184513346193 0.1577224612283107 chr6 171115067 7237281 0.04229482024513949 0.3077545410521484 chr7 159138663 5569660 0.0349987859329948 0.3592492666249866 chr8 146364022 5669813 0.03873775072947913 0.2734491301041321 chr9 141213431 2484170 0.017591598634835236 0.21376393415608172 chr10 135534747 4563519 0.03367047270911274 0.2514466217387056 chr11 135006516 3664691 0.027144549082356886 0.2306027048162513 chr12 133851895 3810029 0.028464512960388048 0.1837123410838896 chr13 115169878 1679451 0.014582380646439514 0.13199844914640807 chr14 107349540 1995293 0.018586879831995553 0.1526036917574566 chr15 102531392 3140471 0.030629360810784663 0.2010368467495149 chr16 90354753 2843285 0.031468018068734026 0.20109625198229442 chr17 81195210 2294796 0.028262701703708877 0.2353631044151277 chr18 78077248 1850838 0.023705215634649418 0.3543030767542377 chr19 59128983 2068694 0.03498612516301862 0.3193190174274706 chr20 63025520 2172302 0.03446702224749593 0.20236858966064158 chr21 48129895 1104196 0.02294199893849758 0.17098013007633833 chr22 51304566 1180356 0.02300684114548401 0.16172955353473425 chrMT 16571 16901 1.0199143081286586 1.2930060282758908 chrX 155270560 3787098 0.024390315846094714 0.19808229018659107 chrY 59373566 225373 0.003795847465183412 0.09499694349137838