BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124984.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,743,892 number of mapped reads = 2,706,343 (98.63%) number of supplementary alignments = 63,870 (2.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,360,064 number of mapped paired reads (second in pair) = 1,346,279 number of mapped paired reads (both in pair) = 2,690,328 number of mapped paired reads (singletons) = 16,015 number of mapped bases = 340,477,791 bp number of sequenced bases = 340,202,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 494,031 duplication rate = 16.4% >>>>>>> Insert size mean insert size = 98,016.9476 std insert size = 3,003,517.3225 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.205 >>>>>>> ACTG content number of A's = 98,933,288 bp (29.08%) number of C's = 67,093,739 bp (19.72%) number of T's = 100,696,696 bp (29.6%) number of G's = 73,476,522 bp (21.6%) number of N's = 2,577 bp (0%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 3,203,904 number of insertions = 69,988 mapped reads with insertion percentage = 2.39% number of deletions = 122,792 mapped reads with deletion percentage = 4.33% homopolymer indels = 44.62% >>>>>>> Coverage mean coverageData = 0.11X std coverageData = 1.7417X There is a 6.5% of reference with a coverageData >= 1X There is a 3.02% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 26998251 0.10831768800287161 1.1254908291713348 chr2 243199373 30117280 0.1238378192693778 1.9586061222828033 chr3 198022430 23792751 0.12015179795541343 0.5130870876609125 chr4 191154276 21552229 0.11274782574050292 1.4270002439612155 chr5 180915260 20785164 0.11488894856077923 0.48644207038266185 chr6 171115067 19637252 0.11476050791015381 0.6661898260172326 chr7 159138663 19489824 0.1224707034267342 1.0922832744847946 chr8 146364022 18711721 0.12784371968132988 0.6259411905910437 chr9 141213431 13665251 0.09677019319784108 1.6951402458256222 chr10 135534747 19582655 0.14448438819899076 6.184102483161915 chr11 135006516 15221443 0.11274598775662058 0.820426147724262 chr12 133851895 15304567 0.11433956164759565 0.4682454109091109 chr13 115169878 10409767 0.09038619455687884 0.4114168868379683 chr14 107349540 10301606 0.09596320580414225 0.4586209617400977 chr15 102531392 9594026 0.09357159610200162 0.4304256609895486 chr16 90354753 11849644 0.13114577381446663 2.497063672637165 chr17 81195210 7895728 0.09724376598077646 1.4064046968398318 chr18 78077248 8441093 0.10811207126562658 1.8617889551734945 chr19 59128983 4674926 0.07906318970512312 0.7109101607624011 chr20 63025520 7167319 0.11372090226308328 0.6489421020706324 chr21 48129895 4185415 0.08696081718025772 0.8965978613454716 chr22 51304566 3180552 0.06199354653930802 0.38412966595762044 chrMT 16571 75405 4.550419407398468 3.7286948120077303 chrX 155270560 12460379 0.08024946261545009 0.4873066675399524 chrY 59373566 5383543 0.09067238777606856 2.6883860824159895