BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472798.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 = 132,786,076 number of mapped reads = 132,301,584 (99.64%) number of supplementary alignments = 90,094 (0.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 66,304,020 number of mapped paired reads (second in pair) = 65,997,564 number of mapped paired reads (both in pair) = 131,952,810 number of mapped paired reads (singletons) = 348,774 number of mapped bases = 13,107,312,756 bp number of sequenced bases = 13,105,767,503 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,187,379 duplication rate = 51.56% >>>>>>> Insert size mean insert size = 11,672.6985 std insert size = 1,073,804.4917 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 53.6609 >>>>>>> ACTG content number of A's = 3,685,284,112 bp (28.12%) number of C's = 2,863,578,097 bp (21.85%) number of T's = 3,744,346,199 bp (28.57%) number of G's = 2,811,243,979 bp (21.45%) number of N's = 1,315,116 bp (0.01%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 50,111,099 number of insertions = 561,787 mapped reads with insertion percentage = 0.42% number of deletions = 666,812 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.97% >>>>>>> Coverage mean coverageData = 4.234X std coverageData = 30.2779X There is a 18.01% of reference with a coverageData >= 1X There is a 10.18% of reference with a coverageData >= 2X There is a 6.5% of reference with a coverageData >= 3X There is a 5.53% of reference with a coverageData >= 4X There is a 4.87% of reference with a coverageData >= 5X There is a 4.6% of reference with a coverageData >= 6X There is a 4.37% of reference with a coverageData >= 7X There is a 4.22% of reference with a coverageData >= 8X There is a 4.09% of reference with a coverageData >= 9X There is a 3.98% of reference with a coverageData >= 10X There is a 3.89% of reference with a coverageData >= 11X There is a 3.8% of reference with a coverageData >= 12X There is a 3.71% of reference with a coverageData >= 13X There is a 3.64% of reference with a coverageData >= 14X There is a 3.56% of reference with a coverageData >= 15X There is a 3.5% of reference with a coverageData >= 16X There is a 3.43% of reference with a coverageData >= 17X There is a 3.37% of reference with a coverageData >= 18X There is a 3.31% of reference with a coverageData >= 19X There is a 3.26% of reference with a coverageData >= 20X There is a 3.2% of reference with a coverageData >= 21X There is a 3.15% of reference with a coverageData >= 22X There is a 3.1% of reference with a coverageData >= 23X There is a 3.06% of reference with a coverageData >= 24X There is a 3.01% of reference with a coverageData >= 25X There is a 2.96% of reference with a coverageData >= 26X There is a 2.92% of reference with a coverageData >= 27X There is a 2.88% of reference with a coverageData >= 28X There is a 2.84% of reference with a coverageData >= 29X There is a 2.8% of reference with a coverageData >= 30X There is a 2.76% of reference with a coverageData >= 31X There is a 2.73% of reference with a coverageData >= 32X There is a 2.69% of reference with a coverageData >= 33X There is a 2.65% of reference with a coverageData >= 34X There is a 2.62% of reference with a coverageData >= 35X There is a 2.59% of reference with a coverageData >= 36X There is a 2.55% of reference with a coverageData >= 37X There is a 2.52% of reference with a coverageData >= 38X There is a 2.49% of reference with a coverageData >= 39X There is a 2.46% of reference with a coverageData >= 40X There is a 2.43% of reference with a coverageData >= 41X There is a 2.4% of reference with a coverageData >= 42X There is a 2.37% of reference with a coverageData >= 43X There is a 2.34% of reference with a coverageData >= 44X There is a 2.32% of reference with a coverageData >= 45X There is a 2.29% of reference with a coverageData >= 46X There is a 2.26% of reference with a coverageData >= 47X There is a 2.24% of reference with a coverageData >= 48X There is a 2.21% of reference with a coverageData >= 49X There is a 2.19% of reference with a coverageData >= 50X There is a 2.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1354088889 5.432639981266084 36.41020549702141 chr2 243199373 1187717040 4.88371752504477 36.27756075288569 chr3 198022430 810329022 4.092107252698596 28.571914897810373 chr4 191154276 640822317 3.3523828522674535 26.964918703404653 chr5 180915260 666792249 3.685660618125856 27.674965734894958 chr6 171115067 673447785 3.9356428209796395 28.333660247838242 chr7 159138663 711038651 4.468044644813938 32.30788570401652 chr8 146364022 481298163 3.288363878112068 25.89694942737723 chr9 141213431 550242509 3.896530982240634 29.248807418693165 chr10 135534747 610239320 4.502456628336053 32.51065066155042 chr11 135006516 638358033 4.728349800538516 29.378172919751666 chr12 133851895 708243378 5.291246552766399 32.18332473806498 chr13 115169878 302852543 2.6296159052977375 23.726056295098346 chr14 107349540 435678193 4.058500790967526 29.925855924435876 chr15 102531392 492361706 4.802058144299846 31.626155194229174 chr16 90354753 463219253 5.126672782781001 33.496074928781624 chr17 81195210 604280405 7.442315932183684 36.36356648811326 chr18 78077248 243917215 3.124049851244757 25.68801158872864 chr19 59128983 488855134 8.267605989434996 36.70095106904063 chr20 63025520 266268280 4.224769268067919 27.356629848578027 chr21 48129895 149228669 3.100540090519624 28.285221242674897 chr22 51304566 201820835 3.933779207877911 26.468159054959994 chrMT 16571 6073415 366.50865970671657 1061.5685688271062 chrX 155270560 345119944 2.2227004526807916 18.460097308295175 chrY 59373566 75019808 1.2635220192096934 20.129443377791496