BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240204.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 = 1,829,546 number of mapped reads = 1,487,610 (81.31%) number of supplementary alignments = 6,835 (0.37%) number of secondary alignments = 0 number of mapped bases = 92,039,734 bp number of sequenced bases = 91,984,158 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,626 duplication rate = 9.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9765 >>>>>>> ACTG content number of A's = 25,190,737 bp (27.39%) number of C's = 15,988,311 bp (17.38%) number of T's = 30,140,024 bp (32.77%) number of G's = 20,642,007 bp (22.44%) number of N's = 23,079 bp (0.03%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 882,246 number of insertions = 6,381 mapped reads with insertion percentage = 0.43% number of deletions = 32,223 mapped reads with deletion percentage = 2.14% homopolymer indels = 50.67% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.3096X There is a 2.03% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 6670085 0.026760555192357975 0.42739559033718993 chr2 243199373 10592187 0.04355351277982119 0.3617563705821324 chr3 198022430 6330800 0.03197011570860937 0.2473471518068736 chr4 191154276 5859138 0.030651357231475166 0.24361963053019395 chr5 180915260 5024183 0.027770918826858497 0.2325845741851098 chr6 171115067 5172907 0.030230575779747085 0.2771663810781362 chr7 159138663 5747964 0.036119217615897654 0.5214078472808723 chr8 146364022 5346481 0.03652865592884568 0.4343057292140496 chr9 141213431 3096715 0.021929323422500795 0.2578552462361559 chr10 135534747 4334333 0.031979496741156715 0.2775982519137446 chr11 135006516 3898131 0.02887365080956537 0.276707055970344 chr12 133851895 4335870 0.032393041577782666 0.2488452726999473 chr13 115169878 1769371 0.015363140351681192 0.1671921105260178 chr14 107349540 3309335 0.0308276588795816 0.24836815005446305 chr15 102531392 2406706 0.02347286965537345 0.21532600947991457 chr16 90354753 2792744 0.030908656238593225 0.24244419968533185 chr17 81195210 2450666 0.030182396227560714 0.25204699035878614 chr18 78077248 2010701 0.025752713517771527 0.41659727843420835 chr19 59128983 1729118 0.02924315474866192 0.32700806318379266 chr20 63025520 1873181 0.029720992385306778 0.23969396180659827 chr21 48129895 1569609 0.03261193484839308 0.2567366185341865 chr22 51304566 833417 0.016244499563645078 0.16986932151691148 chrMT 16571 37390 2.2563514573652768 2.7638563924491515 chrX 155270560 4660114 0.030012862708809707 0.24956312475059814 chrY 59373566 188588 0.0031762956599238118 0.07737301921857645