BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093984.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 353,152 number of mapped reads = 332,608 (94.18%) number of supplementary alignments = 20,477 (5.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 167,230 number of mapped paired reads (second in pair) = 165,378 number of mapped paired reads (both in pair) = 329,402 number of mapped paired reads (singletons) = 3,206 number of mapped bases = 42,004,738 bp number of sequenced bases = 41,188,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 311,171 duplication rate = 49.61% >>>>>>> Insert size mean insert size = 1,092,531.5149 std insert size = 9,520,003.2081 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 41.7139 >>>>>>> ACTG content number of A's = 10,948,413 bp (26.58%) number of C's = 9,613,250 bp (23.34%) number of T's = 10,283,468 bp (24.97%) number of G's = 10,343,206 bp (25.11%) number of N's = 411 bp (0%) GC percentage = 48.45% >>>>>>> Mismatches and indels general error rate = 0.037 number of mismatches = 1,474,713 number of insertions = 23,914 mapped reads with insertion percentage = 7.06% number of deletions = 118,619 mapped reads with deletion percentage = 34.24% homopolymer indels = 28.26% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 2.484X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 833757 0.0033450548554500893 1.123814027331597 chr2 243199373 1872636 0.007700003404202856 2.4106418971868893 chr3 198022430 685787 0.003463178388428018 1.0057297847515954 chr4 191154276 760310 0.003977467917066108 1.1536516530590795 chr5 180915260 604548 0.003341608662530734 1.4179887760723824 chr6 171115067 805424 0.0047069145582603784 1.2817251177214097 chr7 159138663 1043541 0.0065574322438539025 1.9607095481325174 chr8 146364022 455030 0.0031088924298623057 0.970046577831705 chr9 141213431 615305 0.004357269670758159 1.3659218263664121 chr10 135534747 696527 0.005139102816195171 1.5149337808753276 chr11 135006516 838308 0.006209389182371019 1.514084178182728 chr12 133851895 1034640 0.007729737408648567 1.8752907996675203 chr13 115169878 732734 0.0063622017555666766 1.6958855638944408 chr14 107349540 175195 0.0016320051301570552 0.5276677130251146 chr15 102531392 632268 0.006166579694928944 1.692188632413365 chr16 90354753 246410 0.0027271393238162025 0.8005440141568918 chr17 81195210 1003515 0.01235928818953729 2.8667634134868263 chr18 78077248 210872 0.002700812405683151 0.7522620029079924 chr19 59128983 140416 0.0023747406580627304 0.6554233336466522 chr20 63025520 238436 0.003783165930245399 1.1233147766271843 chr21 48129895 169615 0.0035241090802296576 0.8553554755005538 chr22 51304566 133732 0.0026066295931633063 0.598980510224972 chrMT 16571 528570 31.897290447166736 129.70829466903288 chrX 155270560 26977904 0.1737477085160252 8.857056541776492 chrY 59373566 569258 0.009587734716826677 1.3348298915062502