BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524746.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 = 1,401,395 number of mapped reads = 1,274,658 (90.96%) number of supplementary alignments = 4,478 (0.32%) number of secondary alignments = 0 number of mapped bases = 73,301,467 bp number of sequenced bases = 73,275,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,407 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5484 >>>>>>> ACTG content number of A's = 17,062,755 bp (23.29%) number of C's = 13,018,923 bp (17.77%) number of T's = 24,277,845 bp (33.13%) number of G's = 18,906,839 bp (25.8%) number of N's = 9,009 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 381,395 number of insertions = 5,523 mapped reads with insertion percentage = 0.43% number of deletions = 15,787 mapped reads with deletion percentage = 1.23% homopolymer indels = 40.92% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2169X There is a 2.14% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5841287 0.023435395974399597 0.2833368442205917 chr2 243199373 6102659 0.025093234923759446 0.3397216259771686 chr3 198022430 4781463 0.02414606769546258 0.17146072721187933 chr4 191154276 4711996 0.024650225454543324 0.19191066235044787 chr5 180915260 4339990 0.023989076432800637 0.16839085598825532 chr6 171115067 4153051 0.024270516166761635 0.18231991807309705 chr7 159138663 4044948 0.025417757845558876 0.2600569034797412 chr8 146364022 3671126 0.025082161243150315 0.20237137060503893 chr9 141213431 3128867 0.02215700714757083 0.18502589611046585 chr10 135534747 3595823 0.02653063571956201 0.25871417763491855 chr11 135006516 3301588 0.024455027044768714 0.19396715945258922 chr12 133851895 3327554 0.024859969296661805 0.17321987304755762 chr13 115169878 2260698 0.019629247154364444 0.1518476067976094 chr14 107349540 2207935 0.020567717383791304 0.15809299618898326 chr15 102531392 2129120 0.020765542713006374 0.1576273018604722 chr16 90354753 2235336 0.024739550779359666 0.1857786237118466 chr17 81195210 2085311 0.02568268497612113 0.18007841242219894 chr18 78077248 1927380 0.02468555244160245 0.2785584293472596 chr19 59128983 1623804 0.027462065430755 0.2444301326234853 chr20 63025520 1598198 0.025357950239839354 0.18280952397407313 chr21 48129895 959677 0.019939312146847608 0.1668296286338211 chr22 51304566 931597 0.01815816939178474 0.14753594118252536 chrMT 16571 27341 1.6499306016534911 1.6629746572921307 chrX 155270560 4064941 0.026179727824772448 0.1856113301848385 chrY 59373566 249777 0.004206872128920133 0.12459232620116072