BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524954.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 = 1,959,464 number of mapped reads = 1,818,195 (92.79%) number of supplementary alignments = 4,595 (0.23%) number of secondary alignments = 0 number of mapped bases = 106,531,029 bp number of sequenced bases = 106,495,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,906 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4242 >>>>>>> ACTG content number of A's = 27,514,004 bp (25.84%) number of C's = 20,728,985 bp (19.46%) number of T's = 32,966,003 bp (30.96%) number of G's = 25,284,970 bp (23.74%) number of N's = 1,259 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 523,412 number of insertions = 6,390 mapped reads with insertion percentage = 0.35% number of deletions = 20,919 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.0344X std coverageData = 0.3105X There is a 3.09% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 11239169 0.04509183951040186 0.6128244239065123 chr2 243199373 10095371 0.04151067856577081 0.35260430222963973 chr3 198022430 5825203 0.029416884743814122 0.18885482588887603 chr4 191154276 6850088 0.03583538983977528 0.2231306163493773 chr5 180915260 4600095 0.025426793737576364 0.17702202600302447 chr6 171115067 8673597 0.05068868073435053 0.345441344590558 chr7 159138663 6661897 0.041862215469285424 0.4301972243241956 chr8 146364022 7482820 0.051124722440327584 0.30425827066682637 chr9 141213431 2959334 0.020956462703607844 0.2397476903946827 chr10 135534747 5359166 0.03954090090270357 0.2942831056718531 chr11 135006516 4433432 0.03283865202476598 0.2658980125550333 chr12 133851895 4500029 0.033619464259359196 0.20259543892197782 chr13 115169878 2029379 0.017620744549195405 0.14764759787139395 chr14 107349540 2407157 0.022423542755749117 0.16957999481480823 chr15 102531392 2660077 0.025944025026013496 0.19219390837428446 chr16 90354753 3379810 0.03740600120947705 0.22568497425583658 chr17 81195210 2618445 0.03224876196514548 0.2636361764377697 chr18 78077248 2096898 0.026856709908627926 0.38119669250480404 chr19 59128983 2506813 0.04239567252492741 0.37073827602270915 chr20 63025520 2499288 0.03965517460228809 0.21647799917111152 chr21 48129895 1523462 0.031653133670871296 0.20183587686970997 chr22 51304566 1382764 0.026952065046218304 0.17801928888549923 chrMT 16571 24381 1.4713052923782513 1.4831313908074564 chrX 155270560 4446959 0.028640065444473183 0.21697513499268184 chrY 59373566 275395 0.004638343602269063 0.1095950033213413