BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716897.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 = 3,996,505 number of mapped reads = 3,692,397 (92.39%) number of supplementary alignments = 76,754 (1.92%) number of secondary alignments = 0 number of mapped bases = 278,874,625 bp number of sequenced bases = 278,773,894 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 194,919 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4202 >>>>>>> ACTG content number of A's = 71,922,390 bp (25.8%) number of C's = 57,307,749 bp (20.56%) number of T's = 83,415,198 bp (29.92%) number of G's = 66,094,420 bp (23.71%) number of N's = 34,137 bp (0.01%) GC percentage = 44.27% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,025,417 number of insertions = 21,954 mapped reads with insertion percentage = 0.59% number of deletions = 58,284 mapped reads with deletion percentage = 1.56% homopolymer indels = 40.06% >>>>>>> Coverage mean coverageData = 0.0901X std coverageData = 0.6322X There is a 6.88% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 22110696 0.08870868971676504 0.7691813651836443 chr2 243199373 23232938 0.09553041898672987 0.9345947243064507 chr3 198022430 18501088 0.09342925445364952 0.381963850157898 chr4 191154276 17752229 0.09286859478885003 0.447029395941448 chr5 180915260 16337794 0.09030633457896255 0.38654580972265057 chr6 171115067 15955850 0.09324631828008459 0.45406567171485723 chr7 159138663 14817288 0.09310929048084311 0.7813522728013481 chr8 146364022 14378978 0.09824120575205292 0.8267136123702091 chr9 141213431 12131354 0.08590793321918508 0.685676214079913 chr10 135534747 13503419 0.09963067994659701 0.6583843180521912 chr11 135006516 12965734 0.09603783864772868 0.7078492485143987 chr12 133851895 12705958 0.0949254995605404 0.39844830143524496 chr13 115169878 8905895 0.07732833579974792 0.34852164842383754 chr14 107349540 8493150 0.0791167805656177 0.45925376262588 chr15 102531392 7956306 0.07759873190837008 0.35234975339314106 chr16 90354753 8424903 0.0932424993735526 0.4575119239299029 chr17 81195210 7546713 0.09294529812780827 0.4422723498937405 chr18 78077248 7436543 0.09524596717343316 1.353835266226083 chr19 59128983 5766242 0.09751972226547512 0.7182097539474261 chr20 63025520 5916820 0.09387974902864744 0.4129629897719329 chr21 48129895 3742839 0.07776536807321105 0.4017506554117652 chr22 51304566 3497600 0.06817326941231702 0.3323886922254887 chrMT 16571 34048 2.054673827771408 2.1859524348823434 chrX 155270560 16026648 0.10321755779073638 0.5561438293764442 chrY 59373566 733592 0.01235553208981923 0.3196666617179876