BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068105.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 = 5,632,214 number of mapped reads = 5,367,471 (95.3%) number of supplementary alignments = 35,349 (0.63%) number of secondary alignments = 0 number of mapped bases = 352,546,472 bp number of sequenced bases = 352,386,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 757,289 duplication rate = 11.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7103 >>>>>>> ACTG content number of A's = 96,022,943 bp (27.25%) number of C's = 62,936,683 bp (17.86%) number of T's = 115,128,845 bp (32.67%) number of G's = 78,256,403 bp (22.21%) number of N's = 41,973 bp (0.01%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,934,211 number of insertions = 23,501 mapped reads with insertion percentage = 0.43% number of deletions = 90,467 mapped reads with deletion percentage = 1.67% homopolymer indels = 45.5% >>>>>>> Coverage mean coverageData = 0.1139X std coverageData = 1.1496X There is a 7.83% of reference with a coverageData >= 1X There is a 2.25% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 29891586 0.11992582357497918 2.633999755778979 chr2 243199373 25467385 0.10471813593039156 1.2637691715798025 chr3 198022430 29148164 0.14719627468464053 0.520233931055464 chr4 191154276 21152118 0.1106546944312143 0.5111270464787582 chr5 180915260 17669268 0.09766599014367279 0.42990243863792765 chr6 171115067 26468997 0.15468536736160118 0.717619117425164 chr7 159138663 25013963 0.15718344322146277 1.6524815228513656 chr8 146364022 16063218 0.1097484052467484 1.7418266197196464 chr9 141213431 12620324 0.08937056419229698 0.8153015714768687 chr10 135534747 19138538 0.14120761224426087 0.8564250717967233 chr11 135006516 20312130 0.15045296035933556 0.7396571203164275 chr12 133851895 16390969 0.12245601005499399 0.5203804305596669 chr13 115169878 10141107 0.08805346654964764 0.4287116025594087 chr14 107349540 7007970 0.06528178881809833 0.42695040678153884 chr15 102531392 6970451 0.0679835791169206 0.38992818181055533 chr16 90354753 8583598 0.09499885412779557 0.48197588250014184 chr17 81195210 9311663 0.11468241784213626 0.5024133761725843 chr18 78077248 7371633 0.09441461102727391 1.4418805910971435 chr19 59128983 7937745 0.13424457173565796 1.7824941783769452 chr20 63025520 6128593 0.09723986410584157 0.47552510197376896 chr21 48129895 5846176 0.12146662692698582 0.5137180241569088 chr22 51304566 2461586 0.04797986206529844 0.28544530649480876 chrMT 16571 48427 2.9223945446865005 2.471727674369374 chrX 155270560 20363951 0.13115139792115132 0.5728896510817401 chrY 59373566 1036912 0.01746420284070524 0.7456990416230729