BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472512.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 = 16,733,704 number of mapped reads = 16,549,486 (98.9%) number of supplementary alignments = 76,244 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,300,108 number of mapped paired reads (second in pair) = 8,249,378 number of mapped paired reads (both in pair) = 16,451,872 number of mapped paired reads (singletons) = 97,614 number of mapped bases = 1,626,987,773 bp number of sequenced bases = 1,626,769,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,130,773 duplication rate = 44.51% >>>>>>> Insert size mean insert size = 34,932.8571 std insert size = 1,830,426.4581 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 54.9549 >>>>>>> ACTG content number of A's = 449,593,055 bp (27.64%) number of C's = 366,555,994 bp (22.53%) number of T's = 446,450,973 bp (27.44%) number of G's = 363,916,578 bp (22.37%) number of N's = 252,684 bp (0.02%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,742,631 number of insertions = 92,697 mapped reads with insertion percentage = 0.56% number of deletions = 80,696 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.73% >>>>>>> Coverage mean coverageData = 0.5256X std coverageData = 18.0644X There is a 5.76% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 152053571 0.6100428973454795 19.340458008557313 chr2 243199373 130427478 0.5362985783684565 19.327367547657975 chr3 198022430 207913897 1.0499512454220463 26.602927065890878 chr4 191154276 61036415 0.3193044711173503 11.191542086479071 chr5 180915260 89617571 0.495356616130668 19.62950108231635 chr6 171115067 121574213 0.7104822218840612 20.059642058733207 chr7 159138663 71289409 0.4479703904512507 14.83089146037401 chr8 146364022 78811097 0.538459492456418 26.016113618229955 chr9 141213431 88622022 0.6275750215289366 14.983082598088469 chr10 135534747 42036953 0.31015628044076404 9.789075161857333 chr11 135006516 68640959 0.5084270080712252 14.569589292113935 chr12 133851895 99838026 0.7458842924861093 25.960699690325796 chr13 115169878 28525827 0.2476847895940291 8.704581568707711 chr14 107349540 47820426 0.445464656858334 26.268077854331906 chr15 102531392 46036844 0.44900242844649957 16.004810480211187 chr16 90354753 49084557 0.5432426670459716 17.321119502368227 chr17 81195210 49260753 0.606695308750356 13.332907108417185 chr18 78077248 30295292 0.3880169034646303 14.40622933660776 chr19 59128983 34066344 0.576136139530761 15.40489786821681 chr20 63025520 33463872 0.5309574915050285 14.825905926059214 chr21 48129895 6621531 0.13757626107432813 4.664208721324854 chr22 51304566 16858745 0.3286012593888817 11.049496204664962 chrMT 16571 1909 0.115201255204876 0.37730890016550184 chrX 155270560 70149247 0.4517871707295961 12.311485565094419 chrY 59373566 2940815 0.0495307120343757 1.7264751527047257