BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053629.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 11,997,232 number of mapped reads = 9,003,753 (75.05%) number of supplementary alignments = 259 (0%) number of secondary alignments = 0 number of mapped bases = 425,289,347 bp number of sequenced bases = 425,208,933 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,548,307 duplication rate = 19.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5704 >>>>>>> ACTG content number of A's = 125,967,407 bp (29.62%) number of C's = 81,672,135 bp (19.21%) number of T's = 127,636,734 bp (30.02%) number of G's = 89,734,038 bp (21.1%) number of N's = 198,619 bp (0.05%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 2,535,712 number of insertions = 18,075 mapped reads with insertion percentage = 0.2% number of deletions = 54,918 mapped reads with deletion percentage = 0.61% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 0.1374X std coverageData = 1.1197X There is a 5.07% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 1.43% of reference with a coverageData >= 3X There is a 0.98% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 33296567 0.13358669625942476 1.1514656862101476 chr2 243199373 35327877 0.14526302664439847 1.2825257867803141 chr3 198022430 29642997 0.14969514817084106 1.118909674596097 chr4 191154276 28096489 0.1469833141477829 1.1515823525395734 chr5 180915260 26991141 0.14919217428093132 1.1001399786706034 chr6 171115067 25712921 0.1502668435386815 1.1847745894050743 chr7 159138663 22930192 0.14408938448854505 1.157072412139484 chr8 146364022 21590941 0.14751535729183501 1.1627669329213177 chr9 141213431 17712089 0.1254277930546139 1.029218945252986 chr10 135534747 19186585 0.1415621117439353 1.1612281956626056 chr11 135006516 18923766 0.1401692789405809 1.1492943665949542 chr12 133851895 19612734 0.14652563566619659 1.0854678476381447 chr13 115169878 14122005 0.12261891082319284 0.9991971551274234 chr14 107349540 12951322 0.12064627384523492 1.0485274488145346 chr15 102531392 12341897 0.12037188571476724 0.9744605116854649 chr16 90354753 11583756 0.12820306199055184 1.0360871129413471 chr17 81195210 10876095 0.1339499583780866 1.0205591589022613 chr18 78077248 11433578 0.14643930585258333 1.1974686904930432 chr19 59128983 7329434 0.12395670664587619 1.1489270980747566 chr20 63025520 8860479 0.14058557549386344 1.0758371033426735 chr21 48129895 5385673 0.11189870661467265 1.023044903420677 chr22 51304566 4469114 0.08710947871579305 0.8003810568941783 chrMT 16571 52235 3.1521935912135657 6.9105507901336045 chrX 155270560 25789624 0.16609474455427997 1.246658815967988 chrY 59373566 1069836 0.01801872570699223 0.38444987105992434