BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237593.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 = 1,333,507 number of mapped reads = 1,018,282 (76.36%) number of supplementary alignments = 5,189 (0.39%) number of secondary alignments = 0 number of mapped bases = 63,459,198 bp number of sequenced bases = 63,420,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,066 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9521 >>>>>>> ACTG content number of A's = 17,038,329 bp (26.87%) number of C's = 11,091,156 bp (17.49%) number of T's = 20,034,735 bp (31.59%) number of G's = 15,141,116 bp (23.87%) number of N's = 114,842 bp (0.18%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 633,141 number of insertions = 6,211 mapped reads with insertion percentage = 0.6% number of deletions = 23,594 mapped reads with deletion percentage = 2.29% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.2321X There is a 1.76% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 5516058 0.02213056873386887 0.2953953232643224 chr2 243199373 5585211 0.02296556496467612 0.3642699469787039 chr3 198022430 4460315 0.022524291818861127 0.18049249836089384 chr4 191154276 4101556 0.021456783943457274 0.18034750513485226 chr5 180915260 3347302 0.018502043442880384 0.1570368020348757 chr6 171115067 3385921 0.019787392538612628 0.19882471386940678 chr7 159138663 3896381 0.02448418835842551 0.33076942820639005 chr8 146364022 3313044 0.022635644707823074 0.223047318302515 chr9 141213431 2581046 0.01827762403138551 0.22833502749977186 chr10 135534747 2670395 0.01970265971721628 0.21406356217601344 chr11 135006516 2706123 0.020044388079757572 0.21319157801539468 chr12 133851895 3856187 0.028809356789457483 0.20730246638968902 chr13 115169878 2199170 0.019095010242174606 0.17094964825639083 chr14 107349540 1663419 0.01549535284454875 0.161189305995416 chr15 102531392 1954679 0.01906420035729155 0.1677923571569856 chr16 90354753 1693176 0.01873920235275282 0.17869190693953757 chr17 81195210 1344095 0.016553870603943262 0.15862779824064432 chr18 78077248 1679056 0.021505061243961877 0.38851315867371944 chr19 59128983 1126444 0.019050623617186176 0.21636911356679586 chr20 63025520 1297516 0.02058715263277479 0.17271956463764365 chr21 48129895 743896 0.015456007124054602 0.155796883805983 chr22 51304566 612057 0.011929873843977161 0.12748998299511385 chrMT 16571 49956 3.014664172349285 2.4482198452828827 chrX 155270560 3453966 0.022244822199391823 0.1860554488244731 chrY 59373566 222229 0.003742894607340917 0.09874629461849938