BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063539.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 = 4,117,054 number of mapped reads = 3,891,247 (94.52%) number of supplementary alignments = 38,290 (0.93%) number of secondary alignments = 0 number of mapped bases = 252,920,246 bp number of sequenced bases = 252,821,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,002,705 duplication rate = 18.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0833 >>>>>>> ACTG content number of A's = 66,682,029 bp (26.38%) number of C's = 44,965,132 bp (17.79%) number of T's = 82,780,913 bp (32.74%) number of G's = 58,364,572 bp (23.09%) number of N's = 28,702 bp (0.01%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,308,507 number of insertions = 18,184 mapped reads with insertion percentage = 0.46% number of deletions = 56,095 mapped reads with deletion percentage = 1.43% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.0817X std coverageData = 0.8535X There is a 3.89% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 29733805 0.11929280208292842 1.1732562039195467 chr2 243199373 11266402 0.046325785552086926 1.609546360578184 chr3 198022430 14668747 0.07407618924785439 0.4969209282837879 chr4 191154276 11762418 0.061533637887336616 0.5128166196581645 chr5 180915260 12419574 0.06864857060703447 0.47760851513016295 chr6 171115067 22392863 0.13086435573788485 0.8224036470166979 chr7 159138663 21733555 0.13656992330015993 1.0680260575226954 chr8 146364022 8996688 0.061467892703850405 0.9372239614922775 chr9 141213431 10364317 0.07339469713755485 0.6846019208733769 chr10 135534747 16656701 0.12289616772590427 0.7605262908740877 chr11 135006516 9394773 0.06958755235191759 0.5711392658354358 chr12 133851895 9059892 0.06768594497672221 0.48785796206046905 chr13 115169878 6400024 0.05557029417014751 0.4983028187163891 chr14 107349540 7709772 0.07181932964035058 0.5025551398620343 chr15 102531392 3836812 0.03742085155734548 0.3821393909079068 chr16 90354753 5059104 0.05599156471602551 0.449115882271076 chr17 81195210 6640098 0.08177943009199681 0.5493928537488175 chr18 78077248 7805231 0.09996805983735492 1.3333110426208339 chr19 59128983 1801943 0.030474784252588955 0.7889661141660451 chr20 63025520 2856409 0.04532146660590821 0.40538638152525275 chr21 48129895 4764308 0.09898853924364473 0.6049234872371502 chr22 51304566 2692153 0.0524739454963911 0.40020535207310354 chrMT 16571 797193 48.10771830305956 32.57113291658234 chrX 155270560 23322167 0.15020340623489734 0.7940163997125153 chrY 59373566 785297 0.013226374174662173 0.4659110699457064