BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514709.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 73,804,806 number of mapped reads = 72,816,936 (98.66%) number of supplementary alignments = 3,226,995 (4.37%) number of secondary alignments = 0 number of mapped bases = 6,957,813,644 bp number of sequenced bases = 6,952,224,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,551,116 duplication rate = 37.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8502 >>>>>>> ACTG content number of A's = 2,007,526,866 bp (28.88%) number of C's = 1,467,718,657 bp (21.11%) number of T's = 1,987,338,359 bp (28.59%) number of G's = 1,486,502,862 bp (21.38%) number of N's = 3,137,786 bp (0.05%) GC percentage = 42.49% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 41,485,874 number of insertions = 2,233,717 mapped reads with insertion percentage = 2.96% number of deletions = 2,330,004 mapped reads with deletion percentage = 3.06% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 2.2476X std coverageData = 155.9774X There is a 10.09% of reference with a coverageData >= 1X There is a 7.55% of reference with a coverageData >= 2X There is a 6.45% of reference with a coverageData >= 3X There is a 5.8% of reference with a coverageData >= 4X There is a 5.33% of reference with a coverageData >= 5X There is a 4.95% of reference with a coverageData >= 6X There is a 4.63% of reference with a coverageData >= 7X There is a 4.36% of reference with a coverageData >= 8X There is a 4.12% of reference with a coverageData >= 9X There is a 3.91% of reference with a coverageData >= 10X There is a 3.72% of reference with a coverageData >= 11X There is a 3.54% of reference with a coverageData >= 12X There is a 3.38% of reference with a coverageData >= 13X There is a 3.23% of reference with a coverageData >= 14X There is a 3.1% of reference with a coverageData >= 15X There is a 2.97% of reference with a coverageData >= 16X There is a 2.85% of reference with a coverageData >= 17X There is a 2.74% of reference with a coverageData >= 18X There is a 2.64% of reference with a coverageData >= 19X There is a 2.54% of reference with a coverageData >= 20X There is a 2.45% of reference with a coverageData >= 21X There is a 2.37% of reference with a coverageData >= 22X There is a 2.29% of reference with a coverageData >= 23X There is a 2.21% of reference with a coverageData >= 24X There is a 2.14% of reference with a coverageData >= 25X There is a 2.07% of reference with a coverageData >= 26X There is a 2% of reference with a coverageData >= 27X There is a 1.94% of reference with a coverageData >= 28X There is a 1.88% of reference with a coverageData >= 29X There is a 1.83% of reference with a coverageData >= 30X There is a 1.77% of reference with a coverageData >= 31X There is a 1.72% of reference with a coverageData >= 32X There is a 1.67% of reference with a coverageData >= 33X There is a 1.62% of reference with a coverageData >= 34X There is a 1.58% of reference with a coverageData >= 35X There is a 1.54% of reference with a coverageData >= 36X There is a 1.49% of reference with a coverageData >= 37X There is a 1.45% of reference with a coverageData >= 38X There is a 1.42% of reference with a coverageData >= 39X There is a 1.38% of reference with a coverageData >= 40X There is a 1.34% of reference with a coverageData >= 41X There is a 1.31% of reference with a coverageData >= 42X There is a 1.27% of reference with a coverageData >= 43X There is a 1.24% of reference with a coverageData >= 44X There is a 1.21% of reference with a coverageData >= 45X There is a 1.18% of reference with a coverageData >= 46X There is a 1.15% of reference with a coverageData >= 47X There is a 1.13% of reference with a coverageData >= 48X There is a 1.1% of reference with a coverageData >= 49X There is a 1.07% of reference with a coverageData >= 50X There is a 1.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 666878888 2.675535512507309 67.6424361496749 chr2 243199373 421383630 1.732667419335822 18.304179728650837 chr3 198022430 625425158 3.1583551317898686 26.7550525775266 chr4 191154276 463908686 2.4268810288083746 16.666374478015193 chr5 180915260 523950567 2.8961104055014486 21.162635074848655 chr6 171115067 346812691 2.026780558137525 18.6224677426875 chr7 159138663 229508250 1.4421903871342692 13.219995512656224 chr8 146364022 387659000 2.648594884882297 21.35212746416951 chr9 141213431 512699192 3.6306687569966343 530.7412393606164 chr10 135534747 305860554 2.2566947647749696 21.100114390046784 chr11 135006516 331141171 2.4527791754880925 17.53353975740739 chr12 133851895 622801641 4.652916127933788 500.6700597058769 chr13 115169878 127752047 1.1092487829152688 13.994758884201083 chr14 107349540 184074736 1.7147230998847316 14.460220280427437 chr15 102531392 124406363 1.2133490102231324 13.384011093744762 chr16 90354753 82222623 0.9099977618222254 10.387483395978444 chr17 81195210 147884811 1.8213489564224294 16.589667162215505 chr18 78077248 183679511 2.3525356708269225 17.41154223139525 chr19 59128983 157866591 2.6698681930653194 23.159593901611505 chr20 63025520 139459599 2.212748089980059 21.548733359550244 chr21 48129895 156376740 3.249056329750979 21.720643020291188 chr22 51304566 42379301 0.8260337101380022 9.9626473868622 chrMT 16571 3408422 205.6859573954499 96.05645918939223 chrX 155270560 139216514 0.8966059889266839 10.31155402930862 chrY 59373566 31056958 0.5230771889294977 7.063403912198681