BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004005.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 = 2,573,620 number of mapped reads = 2,334,703 (90.72%) number of supplementary alignments = 18,649 (0.72%) number of secondary alignments = 0 number of mapped bases = 152,953,287 bp number of sequenced bases = 152,884,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,390 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2693 >>>>>>> ACTG content number of A's = 40,824,000 bp (26.7%) number of C's = 29,320,261 bp (19.18%) number of T's = 46,467,785 bp (30.39%) number of G's = 36,251,749 bp (23.71%) number of N's = 20,597 bp (0.01%) GC percentage = 42.89% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,261,316 number of insertions = 12,115 mapped reads with insertion percentage = 0.51% number of deletions = 41,592 mapped reads with deletion percentage = 1.76% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.4226X There is a 4.26% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 13428737 0.0538764435014186 0.8041419843791706 chr2 243199373 13819915 0.05682545489128379 0.5489000344402564 chr3 198022430 10311952 0.05207466649106366 0.2588501925840005 chr4 191154276 7346373 0.03843164355894398 0.2418984620590821 chr5 180915260 6831557 0.037761087704818265 0.2190301035629158 chr6 171115067 10333538 0.060389410360923976 0.31870870166005855 chr7 159138663 8977893 0.05641553617928787 0.5720068018604992 chr8 146364022 10394641 0.07101909921551623 0.41111638292766733 chr9 141213431 6479494 0.04588440316275581 0.39588015735959503 chr10 135534747 6394982 0.047183339634669474 0.4011306612164253 chr11 135006516 7316037 0.054190251083881015 0.33925123169086546 chr12 133851895 4619163 0.03450950769131808 0.21778585783259602 chr13 115169878 4544745 0.03946122961074944 0.22237878855550816 chr14 107349540 4541982 0.04231021390496876 0.2707234384442628 chr15 102531392 5211391 0.05082727249036081 0.2639102346724269 chr16 90354753 3454412 0.03823165782988749 0.27329765084313484 chr17 81195210 3882196 0.047813116069285365 0.26191984624238857 chr18 78077248 3967546 0.0508156486253204 0.7478147191460656 chr19 59128983 3020844 0.051089057290229396 0.5903028727090573 chr20 63025520 4264513 0.06766327354379623 0.30705637499423344 chr21 48129895 2292988 0.04764165805888419 0.271510275383069 chr22 51304566 1645614 0.03207539071668592 0.19927792590369903 chrMT 16571 50841 3.068070725967051 2.5961540527461473 chrX 155270560 9403138 0.06055969657094043 0.3072556162709015 chrY 59373566 418795 0.007053559828291264 0.14021278207267715