BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004119.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,859,257 number of mapped reads = 4,123,279 (84.85%) number of supplementary alignments = 28,525 (0.59%) number of secondary alignments = 0 number of mapped bases = 278,480,172 bp number of sequenced bases = 278,362,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 251,770 duplication rate = 4.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.298 >>>>>>> ACTG content number of A's = 78,186,461 bp (28.09%) number of C's = 50,414,027 bp (18.11%) number of T's = 89,977,988 bp (32.32%) number of G's = 59,754,321 bp (21.47%) number of N's = 29,705 bp (0.01%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,594,443 number of insertions = 24,719 mapped reads with insertion percentage = 0.59% number of deletions = 70,283 mapped reads with deletion percentage = 1.69% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.09X std coverageData = 0.7967X There is a 6.85% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 22309936 0.08950804579941248 1.5652018295208434 chr2 243199373 24307691 0.09994964501820487 0.8778827934056574 chr3 198022430 17999921 0.09089839469195485 0.3822433998964586 chr4 191154276 19441850 0.10170763849405075 0.43174710744481926 chr5 180915260 17428397 0.09633458780646807 0.39595495291629557 chr6 171115067 16544134 0.09668426217546348 0.4835856582335543 chr7 159138663 15604973 0.09805896760613102 1.092335148083495 chr8 146364022 14909058 0.10186286080605246 1.2165880452417739 chr9 141213431 11104831 0.07863863176017584 0.7434127093947384 chr10 135534747 13260073 0.09783522892472732 0.7092499831396722 chr11 135006516 12028892 0.08909860321112205 0.6369036346579057 chr12 133851895 12282841 0.09176441618551609 0.4030157008584729 chr13 115169878 8795820 0.07637257373842143 0.3425012938919056 chr14 107349540 8682586 0.08088144578914823 0.42072808557327007 chr15 102531392 7687873 0.07498067518677597 0.3481212947217915 chr16 90354753 7272870 0.08049238981373785 0.48350988322530153 chr17 81195210 6668946 0.08213472198667877 0.4361162954799312 chr18 78077248 8125762 0.10407336590551962 1.6031369549591579 chr19 59128983 4784605 0.08091810068845595 0.9896918881311544 chr20 63025520 5431644 0.08618166101604556 0.39745721168146503 chr21 48129895 4043027 0.08400240640458492 0.43430241922359897 chr22 51304566 2647307 0.05159983226444212 0.27740416659982775 chrMT 16571 58411 3.524892885160823 2.764192960863579 chrX 155270560 16304558 0.10500740127426603 0.4865454458521821 chrY 59373566 754166 0.012702049932456473 0.25909682510753085