BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472752.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 = 18,706,000 number of mapped reads = 18,536,827 (99.1%) number of supplementary alignments = 64,080 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,301,288 number of mapped paired reads (second in pair) = 9,235,539 number of mapped paired reads (both in pair) = 18,433,044 number of mapped paired reads (singletons) = 103,783 number of mapped bases = 1,827,446,917 bp number of sequenced bases = 1,827,182,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,720,875 duplication rate = 46.92% >>>>>>> Insert size mean insert size = 23,292.6988 std insert size = 1,490,002.818 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 55.3739 >>>>>>> ACTG content number of A's = 504,793,160 bp (27.63%) number of C's = 411,807,611 bp (22.54%) number of T's = 501,088,758 bp (27.42%) number of G's = 409,141,742 bp (22.39%) number of N's = 351,267 bp (0.02%) GC percentage = 44.93% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 11,572,419 number of insertions = 110,524 mapped reads with insertion percentage = 0.59% number of deletions = 107,026 mapped reads with deletion percentage = 0.57% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.5903X std coverageData = 19.5819X There is a 5.38% of reference with a coverageData >= 1X There is a 2.28% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% 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 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% 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 0.23% 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 0.22% 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 0.21% 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 0.2% 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 0.19% 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 219667445 0.881311525398366 28.740799694629512 chr2 243199373 138415156 0.5691427337684789 19.469247428962447 chr3 198022430 178475208 0.9012878389584452 19.48928898927016 chr4 191154276 72041608 0.37687677988432755 19.82620344217515 chr5 180915260 91504685 0.5057875438478766 15.760389719209034 chr6 171115067 126576896 0.7397180050778346 19.44257748612211 chr7 159138663 62364110 0.3918853459262756 10.949084217071393 chr8 146364022 95149502 0.6500880523766968 20.076553359209512 chr9 141213431 134896512 0.9552668683476715 25.79262222614357 chr10 135534747 43002329 0.3172790000486001 9.977535855992937 chr11 135006516 74780642 0.553903946384336 17.112609039419997 chr12 133851895 96455783 0.7206157447378687 25.121166343543496 chr13 115169878 32231478 0.27986031208611684 9.761616033737482 chr14 107349540 43147085 0.40193078610304245 19.359329470547856 chr15 102531392 39159198 0.38192398675324724 12.298482186928904 chr16 90354753 55783609 0.6173843339486523 16.877167817708152 chr17 81195210 72001782 0.8867737641173661 23.979798984812078 chr18 78077248 34214356 0.43821160294994005 15.352636219357505 chr19 59128983 46839887 0.7921645971824004 25.977170878738534 chr20 63025520 53217904 0.8443865913363349 33.96830298835481 chr21 48129895 7298107 0.15163355332480988 5.980527062843966 chr22 51304566 18375405 0.3581631506248391 9.536461301505618 chrMT 16571 2342 0.1413312413252067 0.47462954201073393 chrX 155270560 88923810 0.5727023203883596 16.569764639764315 chrY 59373566 2922078 0.049215133886349356 1.5157420469599407