BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714125.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 691,982 number of mapped reads = 495,156 (71.56%) number of supplementary alignments = 18,481 (2.67%) number of secondary alignments = 0 number of mapped bases = 64,008,050 bp number of sequenced bases = 62,890,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,850 duplication rate = 43.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.7914 >>>>>>> ACTG content number of A's = 18,194,104 bp (28.93%) number of C's = 12,448,202 bp (19.79%) number of T's = 17,262,631 bp (27.45%) number of G's = 14,984,680 bp (23.83%) number of N's = 648 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0395 number of mismatches = 2,267,013 number of insertions = 67,853 mapped reads with insertion percentage = 13.21% number of deletions = 190,022 mapped reads with deletion percentage = 36.66% homopolymer indels = 29.99% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 3.4584X There is a 0.07% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4269180 0.017128061638811323 1.5032002083133704 chr2 243199373 7582713 0.031178998968883032 8.538783788032456 chr3 198022430 4024843 0.020325187404275365 1.7175145093606616 chr4 191154276 3415881 0.017869759816411326 1.7133674609630871 chr5 180915260 3433223 0.018976967448738155 1.55940831459779 chr6 171115067 3001211 0.017539139320794 1.4002077069129115 chr7 159138663 2632570 0.0165426173022454 1.3857565279969644 chr8 146364022 2854139 0.01950027719243736 1.743844904390634 chr9 141213431 2304213 0.01631723684980078 1.512503988279975 chr10 135534747 3064806 0.022612695768709407 1.9715124522427296 chr11 135006516 2665350 0.019742380434437698 1.520106639282504 chr12 133851895 2586132 0.01932084711987081 1.746919488863129 chr13 115169878 2076085 0.018026284615843737 1.6652751333300586 chr14 107349540 1979065 0.018435710111100616 1.777286903733654 chr15 102531392 1576003 0.015370931470432002 1.271887337873112 chr16 90354753 1530640 0.016940337383247565 1.4511638139607554 chr17 81195210 1291078 0.015900913366687516 1.3978893280513565 chr18 78077248 1306374 0.01673181411312038 1.3949717048724903 chr19 59128983 878671 0.014860242057604812 1.7461456450248947 chr20 63025520 1191982 0.018912688066675214 1.555732219401324 chr21 48129895 599225 0.012450162212072144 1.159683002390628 chr22 51304566 478909 0.009334627253254613 0.8903000831368159 chrMT 16571 1824350 110.09293343793374 846.1234781456551 chrX 155270560 7088713 0.04565394109482184 2.0173766777358595 chrY 59373566 352694 0.005940252940172063 0.714548455907571