BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472444.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,046,172 number of mapped reads = 17,869,933 (99.02%) number of supplementary alignments = 64,092 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,958,505 number of mapped paired reads (second in pair) = 8,911,428 number of mapped paired reads (both in pair) = 17,777,078 number of mapped paired reads (singletons) = 92,855 number of mapped bases = 1,746,250,500 bp number of sequenced bases = 1,746,051,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,327,708 duplication rate = 48.05% >>>>>>> Insert size mean insert size = 16,839.8935 std insert size = 1,292,623.4257 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.7787 >>>>>>> ACTG content number of A's = 473,054,471 bp (27.09%) number of C's = 401,488,906 bp (22.99%) number of T's = 473,455,949 bp (27.12%) number of G's = 397,835,398 bp (22.78%) number of N's = 216,300 bp (0.01%) GC percentage = 45.78% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 9,550,446 number of insertions = 100,472 mapped reads with insertion percentage = 0.56% number of deletions = 87,310 mapped reads with deletion percentage = 0.47% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.5641X std coverageData = 17.7382X There is a 4.82% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167145582 0.6705924395670814 20.207994342863778 chr2 243199373 138455719 0.5693095228497979 17.039714551516933 chr3 198022430 120702490 0.6095394849967248 14.293979522871105 chr4 191154276 53817789 0.28154112022061173 12.137081510679446 chr5 180915260 61242794 0.3385164634536633 11.974674084144493 chr6 171115067 134816504 0.7878704450964567 17.42658571328767 chr7 159138663 108933995 0.6845224972136407 19.88580867004066 chr8 146364022 133597540 0.9127758186366319 24.821683555924622 chr9 141213431 63522742 0.44983498772152913 11.799266269613344 chr10 135534747 34728810 0.2562354729595651 9.241553904619213 chr11 135006516 48814537 0.3615717111017071 9.608902903473684 chr12 133851895 95270784 0.711762683673623 20.702605835771198 chr13 115169878 85648176 0.7436682011593344 25.924543085759964 chr14 107349540 38687888 0.3603917445757103 11.931437848114346 chr15 102531392 33149819 0.32331384908926236 9.847793789771433 chr16 90354753 107495915 1.1897095773146544 32.917848787548245 chr17 81195210 66320276 0.8168003506610796 19.639083655534595 chr18 78077248 11326288 0.14506515393575348 5.486494552411109 chr19 59128983 49710986 0.8407211400879329 17.070958667090494 chr20 63025520 80959777 1.284555478479194 37.97058341788498 chr21 48129895 15713012 0.3264709386962095 14.98602476800413 chr22 51304566 11851467 0.2310021879923904 6.461714144599662 chrMT 16571 4721 0.28489529901635385 0.650644985952747 chrX 155270560 83948985 0.5406626021056407 17.10954532417674 chrY 59373566 383904 0.006465907740828637 0.518320590657133