BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716740.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 = 731,187 number of mapped reads = 658,148 (90.01%) number of supplementary alignments = 3,716 (0.51%) number of secondary alignments = 0 number of mapped bases = 38,480,631 bp number of sequenced bases = 38,468,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,295 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7057 >>>>>>> ACTG content number of A's = 9,554,320 bp (24.84%) number of C's = 7,435,585 bp (19.33%) number of T's = 12,100,679 bp (31.46%) number of G's = 9,377,672 bp (24.38%) number of N's = 452 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 191,495 number of insertions = 2,498 mapped reads with insertion percentage = 0.38% number of deletions = 7,323 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.44% >>>>>>> Coverage mean coverageData = 0.0124X std coverageData = 0.147X There is a 1.16% of reference with a coverageData >= 1X There is a 0.05% 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 3411239 0.013685979943857392 0.18215048229541667 chr2 243199373 3692141 0.015181539962276136 0.1763896883497378 chr3 198022430 2776491 0.014021093469058025 0.12694420242148444 chr4 191154276 2107202 0.011023567163101284 0.12205754208837928 chr5 180915260 1853319 0.0102441275545247 0.1059553355679695 chr6 171115067 2061087 0.012045035169229137 0.11824792510826974 chr7 159138663 2338238 0.014693085614273384 0.25398801318481995 chr8 146364022 2948205 0.020142962455623144 0.18528078276068594 chr9 141213431 1591788 0.011272213901523291 0.11991312556058141 chr10 135534747 1814476 0.013387533751769204 0.19228161292870913 chr11 135006516 1314478 0.009736404130301385 0.11299792427890264 chr12 133851895 1755517 0.01311536904277672 0.12482425105095286 chr13 115169878 956434 0.008304549910177034 0.09541761707695164 chr14 107349540 1214000 0.011308851439885071 0.11176105685850111 chr15 102531392 894784 0.008726927261457643 0.09750033900350154 chr16 90354753 1185386 0.01311924343371289 0.12334560157323884 chr17 81195210 1610780 0.019838362386155536 0.15018981486506888 chr18 78077248 894026 0.01145053165808303 0.16173736349904755 chr19 59128983 785266 0.013280559890570079 0.17018752112526 chr20 63025520 859079 0.013630653106868456 0.125787073694107 chr21 48129895 394404 0.008194574286937463 0.10000770029860481 chr22 51304566 603206 0.011757355086095066 0.11340578348162204 chrMT 16571 13167 0.7945808943334741 1.0706143920131856 chrX 155270560 1302877 0.008391011148539684 0.1022179141934684 chrY 59373566 103041 0.0017354692827444456 0.06655716183043231