BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068960.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 = 1,647,759 number of mapped reads = 1,305,609 (79.24%) number of supplementary alignments = 5,218 (0.32%) number of secondary alignments = 0 number of mapped bases = 81,109,916 bp number of sequenced bases = 81,069,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,306 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1137 >>>>>>> ACTG content number of A's = 20,772,572 bp (25.62%) number of C's = 13,333,590 bp (16.45%) number of T's = 27,289,610 bp (33.66%) number of G's = 19,491,595 bp (24.04%) number of N's = 182,096 bp (0.22%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 778,494 number of insertions = 7,043 mapped reads with insertion percentage = 0.53% number of deletions = 25,148 mapped reads with deletion percentage = 1.9% homopolymer indels = 49.32% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 0.2976X There is a 2.32% of reference with a coverageData >= 1X There is a 0.2% 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 0.01% 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 8698414 0.03489826410502704 0.545991860819512 chr2 243199373 6304969 0.025925103844737295 0.2948773101860904 chr3 198022430 5056107 0.025533001488770742 0.18115047669803477 chr4 191154276 5519375 0.02887392903520505 0.19467651260225766 chr5 180915260 5177130 0.02861632567645206 0.18600005031926584 chr6 171115067 5461166 0.031915167353439425 0.25446931560902053 chr7 159138663 5071614 0.03186915049047509 0.47873685920734366 chr8 146364022 5039026 0.03442803723991679 0.38668038606883304 chr9 141213431 3052692 0.021617575455694437 0.27780081084526087 chr10 135534747 3846607 0.02838096565746347 0.3538004146582813 chr11 135006516 2820072 0.020888414008106097 0.2128835310103689 chr12 133851895 3198567 0.023896314654342398 0.1771849316314144 chr13 115169878 1475857 0.012814609389444695 0.12426362155496368 chr14 107349540 1944045 0.018109486076978067 0.17638787600177389 chr15 102531392 1510477 0.014731849149185452 0.13663074510570616 chr16 90354753 1648230 0.018241763109019843 0.16483481634356673 chr17 81195210 1701076 0.020950447692665613 0.17745028514176797 chr18 78077248 1777096 0.022760740747419787 0.3961261616494759 chr19 59128983 1401843 0.0237082210597128 0.38447764853228156 chr20 63025520 1276574 0.020254874533363627 0.16349392160860685 chr21 48129895 1225409 0.025460454463904398 0.1823968800445146 chr22 51304566 755145 0.014718865373503013 0.13208910965626203 chrMT 16571 118956 7.178564962886972 5.2679259927851545 chrX 155270560 6789847 0.04372913319820576 0.27712555065240996 chrY 59373566 239622 0.004035836419190318 0.08980304715775098