BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238334.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 = 2,890,354 number of mapped reads = 2,578,300 (89.2%) number of supplementary alignments = 24,517 (0.85%) number of secondary alignments = 0 number of mapped bases = 168,429,727 bp number of sequenced bases = 168,351,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,058 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.714 >>>>>>> ACTG content number of A's = 48,139,165 bp (28.59%) number of C's = 32,644,457 bp (19.39%) number of T's = 50,964,659 bp (30.27%) number of G's = 36,551,765 bp (21.71%) number of N's = 51,764 bp (0.03%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,458,273 number of insertions = 12,540 mapped reads with insertion percentage = 0.48% number of deletions = 45,177 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.5288X There is a 4.53% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% 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 17371673 0.06969560569319504 1.0908062572556128 chr2 243199373 13212697 0.05432866391477086 0.6232675976964701 chr3 198022430 9798136 0.049479930127107316 0.25641314105544005 chr4 191154276 7514821 0.039312858478771355 0.2575116617164332 chr5 180915260 12974826 0.0717176981090484 0.31478536870091817 chr6 171115067 11862599 0.06932527455340914 0.4198534286190791 chr7 159138663 7957351 0.050002625697565396 0.5878637938762825 chr8 146364022 7577474 0.05177142508423279 0.7607744778847418 chr9 141213431 6756536 0.04784627037353125 0.4869554590745923 chr10 135534747 8164821 0.06024153348661211 0.47589903334004596 chr11 135006516 6859750 0.05081051050898906 0.3849072868183529 chr12 133851895 8008733 0.05983279504559872 0.29502848984584007 chr13 115169878 2954404 0.025652575580569773 0.18438717165646382 chr14 107349540 4393322 0.04092539194858218 0.2858169073021003 chr15 102531392 4403744 0.04295020202203048 0.24918372109837605 chr16 90354753 4330811 0.04793119184333335 0.30465522408311735 chr17 81195210 5202685 0.06407625523722398 0.3502402066427083 chr18 78077248 5863649 0.075100610615784 0.8456836434727782 chr19 59128983 3813698 0.06449794680216299 0.7948904041777987 chr20 63025520 3645639 0.05784385436248681 0.28437178606065616 chr21 48129895 2216710 0.04605682185676906 0.28147798268957913 chr22 51304566 1924328 0.037507928631537395 0.22139024825884954 chrMT 16571 5028 0.30342164021483314 0.6119914887828392 chrX 155270560 11185782 0.07204058515664528 0.3691980594724486 chrY 59373566 430510 0.007250869856797889 0.16594589985065855