BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716627.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 894,326 number of mapped reads = 807,717 (90.32%) number of supplementary alignments = 3,434 (0.38%) number of secondary alignments = 0 number of mapped bases = 47,038,239 bp number of sequenced bases = 47,024,432 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,640 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2787 >>>>>>> ACTG content number of A's = 12,107,439 bp (25.75%) number of C's = 8,872,907 bp (18.87%) number of T's = 14,998,694 bp (31.9%) number of G's = 11,043,883 bp (23.49%) number of N's = 1,509 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 233,263 number of insertions = 3,857 mapped reads with insertion percentage = 0.48% number of deletions = 8,701 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 0.1658X There is a 1.41% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3771101 0.015129755684741102 0.27875020359077124 chr2 243199373 3904986 0.016056727251513102 0.20627447807704888 chr3 198022430 3094970 0.015629391074536356 0.13285845826142947 chr4 191154276 3032656 0.015864965531819965 0.13912774527855773 chr5 180915260 2954691 0.01633190588787259 0.13550841710096934 chr6 171115067 2657793 0.015532197407256955 0.14448321220245414 chr7 159138663 2486755 0.015626340910002492 0.18241913473292062 chr8 146364022 2314045 0.015810203685165197 0.15374698005525886 chr9 141213431 1986009 0.014063881784729103 0.1417852521623289 chr10 135534747 2276761 0.016798356512961212 0.16710028177848607 chr11 135006516 2055438 0.01522473181961084 0.14588684731811782 chr12 133851895 2159811 0.016135826840553882 0.13518146433298142 chr13 115169878 1505381 0.013070961141419287 0.12116710626620651 chr14 107349540 1439908 0.01341326660552062 0.12458954774655903 chr15 102531392 1357055 0.013235507423911693 0.12283379705135729 chr16 90354753 1378811 0.015259971990626769 0.1350300123015127 chr17 81195210 1338600 0.016486194197908966 0.14031590925407011 chr18 78077248 1234906 0.01581646422783754 0.2184327968051501 chr19 59128983 1012130 0.0171173246798444 0.20473931266092374 chr20 63025520 1007360 0.015983366737791296 0.13432556334198087 chr21 48129895 635592 0.013205763278727287 0.12600693788469766 chr22 51304566 579630 0.011297824836877092 0.11244960407145585 chrMT 16571 3985 0.24048035725061856 0.5175203697598143 chrX 155270560 2705684 0.017425608563529364 0.14708634120369063 chrY 59373566 144181 0.0024283702279226417 0.07263067431137175