BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236086.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 = 1,432,050 number of mapped reads = 1,285,632 (89.78%) number of supplementary alignments = 6,823 (0.48%) number of secondary alignments = 0 number of mapped bases = 84,615,092 bp number of sequenced bases = 84,573,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,013 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5817 >>>>>>> ACTG content number of A's = 23,231,673 bp (27.47%) number of C's = 14,984,429 bp (17.72%) number of T's = 27,298,439 bp (32.28%) number of G's = 19,014,524 bp (22.48%) number of N's = 44,375 bp (0.05%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 660,401 number of insertions = 6,086 mapped reads with insertion percentage = 0.47% number of deletions = 24,238 mapped reads with deletion percentage = 1.86% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.265X There is a 2.43% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 7634045 0.030627987883729283 0.39876366584782524 chr2 243199373 7744938 0.031846044274135524 0.31180060016474614 chr3 198022430 7199217 0.03635556335714091 0.20807876934426736 chr4 191154276 3671384 0.019206392223211372 0.16437667240263928 chr5 180915260 3541882 0.019577574605923236 0.15436260244627725 chr6 171115067 8295972 0.048481832403455154 0.31131420685577144 chr7 159138663 4308572 0.027074325740690682 0.3329539112362491 chr8 146364022 5101250 0.03485316903904158 0.46540974641704946 chr9 141213431 3327960 0.023566880122047315 0.2518756133235339 chr10 135534747 3563011 0.02628854281920783 0.24945290636661085 chr11 135006516 3013969 0.02232461876136408 0.19964622632263543 chr12 133851895 2942466 0.02198299844764992 0.17205520027693064 chr13 115169878 2921583 0.02536759655159138 0.1747080456244862 chr14 107349540 2834217 0.026401761945137353 0.1896018224981074 chr15 102531392 2049386 0.019987888197206958 0.16019514568650278 chr16 90354753 1893318 0.02095427121581529 0.16700983146212342 chr17 81195210 2555708 0.0314760932325934 0.215233690740817 chr18 78077248 2672297 0.03422632160395817 0.38778964452939263 chr19 59128983 1394155 0.023578200220355557 0.26681372054676483 chr20 63025520 1116732 0.017718727271111765 0.1495295312508531 chr21 48129895 1179457 0.024505704822335474 0.18323691371462125 chr22 51304566 615740 0.012001660826835568 0.11744299105120959 chrMT 16571 40489 2.4433649146098606 2.3259367143689973 chrX 155270560 4810723 0.03098284053332454 0.2045006022299486 chrY 59373566 186621 0.0031431664387481795 0.08936066374321681