BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472550.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 = 14,283,196 number of mapped reads = 14,095,654 (98.69%) number of supplementary alignments = 47,402 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,072,095 number of mapped paired reads (second in pair) = 7,023,559 number of mapped paired reads (both in pair) = 14,003,702 number of mapped paired reads (singletons) = 91,952 number of mapped bases = 1,387,641,813 bp number of sequenced bases = 1,387,443,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,513,140 duplication rate = 45.41% >>>>>>> Insert size mean insert size = 24,385.2232 std insert size = 1,579,128.7533 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 54.9863 >>>>>>> ACTG content number of A's = 381,533,283 bp (27.5%) number of C's = 314,679,517 bp (22.68%) number of T's = 379,121,918 bp (27.33%) number of G's = 311,893,613 bp (22.48%) number of N's = 214,715 bp (0.02%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 8,518,944 number of insertions = 71,485 mapped reads with insertion percentage = 0.5% number of deletions = 73,039 mapped reads with deletion percentage = 0.51% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.4482X std coverageData = 14.7027X There is a 4.74% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166664533 0.6686624584177064 21.658271695417312 chr2 243199373 95239533 0.39161093149693277 12.410280518126557 chr3 198022430 173025881 0.8737691028233519 21.69913292541613 chr4 191154276 54969830 0.2875678805113415 11.226952876787779 chr5 180915260 69217544 0.38259649296582277 12.508971094827485 chr6 171115067 96847937 0.5659813521856611 16.754468418899684 chr7 159138663 62718794 0.3941141192068454 12.970719481973742 chr8 146364022 60125078 0.4107913760391198 12.650418102134669 chr9 141213431 70154259 0.49679593862428 13.905398556953754 chr10 135534747 25796683 0.19033261632900675 6.2450593083133015 chr11 135006516 73609368 0.5452282614270262 16.638104072701648 chr12 133851895 74472141 0.5563771883842212 16.861517428140278 chr13 115169878 35593968 0.30905622735833754 13.151381135067524 chr14 107349540 49089486 0.45728641221937233 16.26816239169975 chr15 102531392 21293494 0.20767780076564257 7.646636688272399 chr16 90354753 46724361 0.5171212299147119 15.86527746666137 chr17 81195210 38139901 0.46973092378232656 11.619706247998208 chr18 78077248 26709501 0.3420907073978837 10.973272296870169 chr19 59128983 20612305 0.3485990110805728 9.202834623544879 chr20 63025520 30061100 0.47696710792707464 13.947547080898639 chr21 48129895 8827199 0.18340366211062792 10.462947071751586 chr22 51304566 11489668 0.22395020357447326 8.407330900016316 chrMT 16571 2602 0.15702130227505884 0.4586209181339365 chrX 155270560 73635793 0.47424182021369665 15.868131478821807 chrY 59373566 2620854 0.04414176504069168 1.5188525456077884