BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716777.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 = 1,095,267 number of mapped reads = 1,025,344 (93.62%) number of supplementary alignments = 19,455 (1.78%) number of secondary alignments = 0 number of mapped bases = 78,818,313 bp number of sequenced bases = 78,787,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,627 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3765 >>>>>>> ACTG content number of A's = 19,427,668 bp (24.66%) number of C's = 15,716,800 bp (19.95%) number of T's = 23,964,245 bp (30.42%) number of G's = 19,675,979 bp (24.97%) number of N's = 2,630 bp (0%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 506,910 number of insertions = 7,078 mapped reads with insertion percentage = 0.68% number of deletions = 14,698 mapped reads with deletion percentage = 1.41% homopolymer indels = 39.03% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2513X There is a 2.23% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.04% 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 9013164 0.036161049323925255 0.47337504652157464 chr2 243199373 7588120 0.031201231756465095 0.26535328955213633 chr3 198022430 5219034 0.026355771919372974 0.18408455421995687 chr4 191154276 4019060 0.021025216302250023 0.22664043091358474 chr5 180915260 4999959 0.027637021885273803 0.18595572767007765 chr6 171115067 5065960 0.029605575293962863 0.19904028321041964 chr7 159138663 5046132 0.031709025983208114 0.3078009663237136 chr8 146364022 5058859 0.034563541851835695 0.2698074880206831 chr9 141213431 2409019 0.017059418377845376 0.17294355781576695 chr10 135534747 3428651 0.02529721031611178 0.341815090577898 chr11 135006516 3490321 0.025852981792375117 0.2247868879511017 chr12 133851895 2786058 0.02081448305233183 0.16000790475929122 chr13 115169878 1522937 0.01322339683298093 0.12497360739464047 chr14 107349540 1556401 0.014498441260204747 0.13993779251014385 chr15 102531392 1595211 0.015558269217685057 0.13621639823771645 chr16 90354753 2433452 0.026932196914975795 0.193144494449441 chr17 81195210 1546723 0.019049436536958276 0.16973067085070837 chr18 78077248 2340271 0.029973789547500445 0.26535600758696626 chr19 59128983 2029451 0.03432244048574284 0.3378315118130229 chr20 63025520 2123039 0.033685386491059496 0.21135034810836603 chr21 48129895 1209405 0.02512793763626536 0.21253952162852058 chr22 51304566 1220515 0.023789597986268902 0.17406198384396268 chrMT 16571 75119 4.53316034035363 3.4670722058755126 chrX 155270560 2792214 0.017982893859595794 0.15595625266462532 chrY 59373566 249238 0.0041977940149325035 0.18634748731782344