BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716214.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 = 555,549 number of mapped reads = 486,115 (87.5%) number of supplementary alignments = 2,198 (0.4%) number of secondary alignments = 0 number of mapped bases = 27,584,558 bp number of sequenced bases = 27,576,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,726 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8943 >>>>>>> ACTG content number of A's = 6,971,548 bp (25.28%) number of C's = 5,336,257 bp (19.35%) number of T's = 8,192,846 bp (29.71%) number of G's = 7,075,063 bp (25.66%) number of N's = 575 bp (0%) GC percentage = 45.01% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 139,800 number of insertions = 1,584 mapped reads with insertion percentage = 0.32% number of deletions = 4,802 mapped reads with deletion percentage = 0.98% homopolymer indels = 40.31% >>>>>>> Coverage mean coverageData = 0.0089X std coverageData = 0.1077X There is a 0.85% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2224955 0.008926577559058518 0.1398920797243423 chr2 243199373 2338173 0.009614222977458087 0.11668442712062618 chr3 198022430 1823631 0.00920921432991202 0.09857284603996502 chr4 191154276 1783555 0.009330447831572442 0.10197979787480027 chr5 180915260 1631173 0.00901622671299259 0.09801315651449317 chr6 171115067 1579198 0.00922886586018752 0.10016370121392644 chr7 159138663 1498923 0.009418974444946795 0.11434649521752419 chr8 146364022 1380764 0.009433766448424053 0.10398570318937593 chr9 141213431 1151918 0.008157283566037002 0.10610234381705365 chr10 135534747 1305591 0.00963288771992912 0.10865642565144401 chr11 135006516 1256192 0.009304676820191404 0.10999175374982896 chr12 133851895 1239855 0.00926288716345779 0.09942860184088362 chr13 115169878 865712 0.007516826578560759 0.08878029710453164 chr14 107349540 841721 0.00784093718519893 0.09356310523540606 chr15 102531392 820006 0.007997609161494657 0.09213145144753078 chr16 90354753 831569 0.009203378598135286 0.1016230180293904 chr17 81195210 770493 0.009489389829769514 0.10137112268330514 chr18 78077248 734381 0.009405825881567957 0.15114961436457755 chr19 59128983 575289 0.009729391083895355 0.12342551423662058 chr20 63025520 607773 0.009643284180757255 0.1015562521575434 chr21 48129895 362502 0.007531743005049149 0.0928714891374177 chr22 51304566 342590 0.0066775732982518555 0.08393033502000259 chrMT 16571 6140 0.3705268239695854 0.6438058667746465 chrX 155270560 1531761 0.009865109007142114 0.10710181046475876 chrY 59373566 80693 0.0013590728237545982 0.04465772948284628