BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438298.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 780,930,134 number of mapped reads = 776,744,186 (99.46%) number of supplementary alignments = 20,611,699 (2.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 388,628,729 number of mapped paired reads (second in pair) = 388,115,457 number of mapped paired reads (both in pair) = 774,154,076 number of mapped paired reads (singletons) = 2,590,110 number of mapped bases = 110,022,493,620 bp number of sequenced bases = 109,987,348,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 320,948,461 duplication rate = 36.43% >>>>>>> Insert size mean insert size = 103,785.9631 std insert size = 3,109,422.5392 median insert size = 459 >>>>>>> Mapping quality mean mapping quality = 54.2442 >>>>>>> ACTG content number of A's = 33,865,364,442 bp (30.79%) number of C's = 20,791,882,980 bp (18.9%) number of T's = 31,886,674,770 bp (28.99%) number of G's = 23,443,222,713 bp (21.31%) number of N's = 204,060 bp (0%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 613,826,323 number of insertions = 14,587,965 mapped reads with insertion percentage = 1.83% number of deletions = 12,941,529 mapped reads with deletion percentage = 1.62% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 35.5405X std coverageData = 106.6368X There is a 90.91% of reference with a coverageData >= 1X There is a 90.19% of reference with a coverageData >= 2X There is a 89.44% of reference with a coverageData >= 3X There is a 88.65% of reference with a coverageData >= 4X There is a 87.79% of reference with a coverageData >= 5X There is a 86.86% of reference with a coverageData >= 6X There is a 85.86% of reference with a coverageData >= 7X There is a 84.79% of reference with a coverageData >= 8X There is a 83.64% of reference with a coverageData >= 9X There is a 82.42% of reference with a coverageData >= 10X There is a 81.12% of reference with a coverageData >= 11X There is a 79.76% of reference with a coverageData >= 12X There is a 78.33% of reference with a coverageData >= 13X There is a 76.84% of reference with a coverageData >= 14X There is a 75.3% of reference with a coverageData >= 15X There is a 73.72% of reference with a coverageData >= 16X There is a 72.09% of reference with a coverageData >= 17X There is a 70.43% of reference with a coverageData >= 18X There is a 68.74% of reference with a coverageData >= 19X There is a 67.03% of reference with a coverageData >= 20X There is a 65.3% of reference with a coverageData >= 21X There is a 63.56% of reference with a coverageData >= 22X There is a 61.82% of reference with a coverageData >= 23X There is a 60.08% of reference with a coverageData >= 24X There is a 58.35% of reference with a coverageData >= 25X There is a 56.62% of reference with a coverageData >= 26X There is a 54.91% of reference with a coverageData >= 27X There is a 53.22% of reference with a coverageData >= 28X There is a 51.55% of reference with a coverageData >= 29X There is a 49.9% of reference with a coverageData >= 30X There is a 48.29% of reference with a coverageData >= 31X There is a 46.7% of reference with a coverageData >= 32X There is a 45.14% of reference with a coverageData >= 33X There is a 43.61% of reference with a coverageData >= 34X There is a 42.12% of reference with a coverageData >= 35X There is a 40.66% of reference with a coverageData >= 36X There is a 39.24% of reference with a coverageData >= 37X There is a 37.85% of reference with a coverageData >= 38X There is a 36.51% of reference with a coverageData >= 39X There is a 35.2% of reference with a coverageData >= 40X There is a 33.93% of reference with a coverageData >= 41X There is a 32.69% of reference with a coverageData >= 42X There is a 31.5% of reference with a coverageData >= 43X There is a 30.34% of reference with a coverageData >= 44X There is a 29.21% of reference with a coverageData >= 45X There is a 28.13% of reference with a coverageData >= 46X There is a 27.08% of reference with a coverageData >= 47X There is a 26.06% of reference with a coverageData >= 48X There is a 25.08% of reference with a coverageData >= 49X There is a 24.14% of reference with a coverageData >= 50X There is a 23.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8616289831 34.56877979453459 42.49927960490459 chr2 243199373 9393777701 38.625830260672586 228.51486601952084 chr3 198022430 7936668837 40.079645709831965 28.89680384640029 chr4 191154276 7733530971 40.457012695860385 37.63175687808701 chr5 180915260 7064823820 39.050458319546955 28.80335831034845 chr6 171115067 6735581043 39.362875292565555 33.54370738998111 chr7 159138663 5905978665 37.11215460569755 31.43285803642672 chr8 146364022 5654271764 38.63156865148185 32.23273642959491 chr9 141213431 4648181120 32.91599876218573 56.50484256670451 chr10 135534747 4943598793 36.4747705103253 81.69560989140709 chr11 135006516 4870813169 36.07835616615719 31.563342886034224 chr12 133851895 5069301579 37.872467767452974 31.027901965588292 chr13 115169878 3804511010 33.033906747734854 29.59104064673907 chr14 107349540 3322086414 30.946442937715428 30.29897472370098 chr15 102531392 3022272165 29.47655450732591 29.063801315396834 chr16 90354753 2838310283 31.412960455992835 90.34106259288389 chr17 81195210 2426886354 29.88952616786138 51.73832757899618 chr18 78077248 3000763854 38.433268728938806 68.26256427883501 chr19 59128983 1428267892 24.155123588038034 30.439470036054445 chr20 63025520 2106931705 33.42981866710501 33.131326943245455 chr21 48129895 1408090028 29.256037811842308 45.60817119837498 chr22 51304566 983969626 19.17898742189925 26.727495224415865 chrMT 16571 500719723 30216.626817934946 11026.787216921126 chrX 155270560 6467827279 41.65520675007548 32.50048789475581 chrY 59373566 139039994 2.3417827724883495 37.75319906290809