BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006078.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 14,331,294 number of mapped reads = 12,106,828 (84.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,168,272 number of mapped paired reads (second in pair) = 5,938,556 number of mapped paired reads (both in pair) = 10,714,560 number of mapped paired reads (singletons) = 1,392,268 number of mapped bases = 466,194,021 bp number of sequenced bases = 466,143,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,154,226 duplication rate = 15.8% >>>>>>> Insert size mean insert size = 93,035.2983 std insert size = 2,989,297.2838 median insert size = 106 >>>>>>> Mapping quality mean mapping quality = 46.2593 >>>>>>> ACTG content number of A's = 124,013,441 bp (26.6%) number of C's = 102,269,231 bp (21.94%) number of T's = 129,636,805 bp (27.81%) number of G's = 110,204,944 bp (23.64%) number of N's = 18,819 bp (0%) GC percentage = 45.58% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,144,897 number of insertions = 16,147 mapped reads with insertion percentage = 0.13% number of deletions = 40,163 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.1506X std coverageData = 1.0233X There is a 4.54% of reference with a coverageData >= 1X There is a 2.91% of reference with a coverageData >= 2X There is a 2.07% of reference with a coverageData >= 3X There is a 1.52% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% 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 39379581 0.15799190726991208 1.1274663147931259 chr2 243199373 40025658 0.1645796101620706 1.0830274086694167 chr3 198022430 32394416 0.16358962972022917 0.9793637791145073 chr4 191154276 28464308 0.14890751384499504 0.9497540217970689 chr5 180915260 28053794 0.15506593528926194 0.9571748586183627 chr6 171115067 26700458 0.1560380302454605 1.0888735341202416 chr7 159138663 25437355 0.15984396576211024 1.1611212032680038 chr8 146364022 23164774 0.1582682252336575 1.0705595338966003 chr9 141213431 20000124 0.14163046573098276 0.936338427896914 chr10 135534747 22783576 0.16810136517980884 1.0265019762950307 chr11 135006516 21995867 0.16292448432637133 1.3417192085760554 chr12 133851895 21497753 0.16060850688740716 0.9747615208131213 chr13 115169878 14292467 0.12409900269235329 0.8595946813880474 chr14 107349540 14360301 0.13377142556921995 0.8948477546868607 chr15 102531392 14447302 0.1409061334113166 0.9294137744449383 chr16 90354753 14928959 0.1652260506981852 1.0256643590252457 chr17 81195210 14023973 0.17271921582566263 1.0779067584778417 chr18 78077248 11990083 0.15356692643675146 1.0736525159464185 chr19 59128983 11192179 0.1892841451374193 1.2842852933699804 chr20 63025520 11006082 0.17462897569111688 1.0418547439127985 chr21 48129895 6113032 0.12701112271281706 0.9152476902336882 chr22 51304566 6763571 0.13183175548156864 0.9105429585719279 chrMT 16571 54873 3.3113873634662965 5.397745579807275 chrX 155270560 14049211 0.09048213003160419 0.7283533510440446 chrY 59373566 3074324 0.0517793389738457 0.5322779900319999