BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004085.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 = 2,003,430 number of mapped reads = 1,775,916 (88.64%) number of supplementary alignments = 15,173 (0.76%) number of secondary alignments = 0 number of mapped bases = 115,882,395 bp number of sequenced bases = 115,816,964 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,302 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2243 >>>>>>> ACTG content number of A's = 32,981,717 bp (28.48%) number of C's = 20,455,522 bp (17.66%) number of T's = 37,080,465 bp (32.02%) number of G's = 25,255,123 bp (21.81%) number of N's = 44,137 bp (0.04%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,006,751 number of insertions = 9,314 mapped reads with insertion percentage = 0.52% number of deletions = 39,283 mapped reads with deletion percentage = 2.18% homopolymer indels = 44.07% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.3666X There is a 3.19% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% 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 8724517 0.035002990022640706 0.6300089271836834 chr2 243199373 9390879 0.038613911229121466 0.39946499616385467 chr3 198022430 7460129 0.03767315147077026 0.22205611963562596 chr4 191154276 7498395 0.03922692788729455 0.2330343975973601 chr5 180915260 6721047 0.03715024923823452 0.22034619690610904 chr6 171115067 8163489 0.0477075990041251 0.28938191716680095 chr7 159138663 8917309 0.05603483673857433 0.5442407852188982 chr8 146364022 7870230 0.053771616087456245 0.6848006259457501 chr9 141213431 3470937 0.02457936879955845 0.2754515993213371 chr10 135534747 4000988 0.029520016737848043 0.3223726628933364 chr11 135006516 5658776 0.041914836169833464 0.3145745965916896 chr12 133851895 5404790 0.04037888294371925 0.2324979107571243 chr13 115169878 3277612 0.028458934375184455 0.18898154117348157 chr14 107349540 2969694 0.027663779462864954 0.2003486444620367 chr15 102531392 2517040 0.024548969353698036 0.1805142626366878 chr16 90354753 3494122 0.03867114771483023 0.2538267978095362 chr17 81195210 2124772 0.026168686551829842 0.20417261490480362 chr18 78077248 3492027 0.04472528283783773 0.4913937845136243 chr19 59128983 1376803 0.023284740074085156 0.44811346738386654 chr20 63025520 3312894 0.052564326323686024 0.2882162552801715 chr21 48129895 1684573 0.035000554229341244 0.22517961188126334 chr22 51304566 640833 0.012490759594379962 0.12301316774849522 chrMT 16571 3159 0.19063424054070363 0.49368631162746457 chrX 155270560 7403434 0.04768086107244026 0.28309285599062417 chrY 59373566 303946 0.005119214163420806 0.12313952669950362