BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472400.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 = 22,013,022 number of mapped reads = 21,844,006 (99.23%) number of supplementary alignments = 109,467 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,952,785 number of mapped paired reads (second in pair) = 10,891,221 number of mapped paired reads (both in pair) = 21,739,314 number of mapped paired reads (singletons) = 104,692 number of mapped bases = 2,142,591,512 bp number of sequenced bases = 2,142,356,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,340,747 duplication rate = 45.76% >>>>>>> Insert size mean insert size = 19,818.2789 std insert size = 1,447,872.6225 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.9957 >>>>>>> ACTG content number of A's = 569,530,151 bp (26.58%) number of C's = 502,768,968 bp (23.47%) number of T's = 571,208,019 bp (26.66%) number of G's = 498,583,613 bp (23.27%) number of N's = 265,757 bp (0.01%) GC percentage = 46.74% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 11,381,514 number of insertions = 136,660 mapped reads with insertion percentage = 0.62% number of deletions = 102,842 mapped reads with deletion percentage = 0.46% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.6921X std coverageData = 32.119X There is a 5.32% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 197207200 0.7912004359660151 32.48575558698297 chr2 243199373 149438479 0.6144690142766116 23.67091815181098 chr3 198022430 149247002 0.7536873575382345 32.15726201164605 chr4 191154276 56635810 0.29628324924314015 12.03905984992947 chr5 180915260 107409160 0.5936987294493565 27.7250420282983 chr6 171115067 223793439 1.307853498371362 54.55079552204555 chr7 159138663 102848697 0.6462835307344513 22.222354211650906 chr8 146364022 101909288 0.6962728039818419 25.071579095932428 chr9 141213431 131523907 0.9313838355786427 51.43531118110568 chr10 135534747 60255278 0.4445743939006283 17.124668315566794 chr11 135006516 91568403 0.6782517297165124 37.311155320422074 chr12 133851895 114297037 0.8539067526836285 27.611893576934612 chr13 115169878 64428669 0.5594229161204808 30.315860018168745 chr14 107349540 43090377 0.40140253046263635 16.032246237562358 chr15 102531392 36137726 0.3524552363436166 16.305393435145117 chr16 90354753 162289957 1.7961418919489494 79.02731334613333 chr17 81195210 107836028 1.3281082467795822 38.633943265035256 chr18 78077248 23338388 0.29891407033198714 11.366092970400599 chr19 59128983 60595186 1.0247966889604714 27.94749718780473 chr20 63025520 46988020 0.745539584600016 23.60916014306172 chr21 48129895 19462684 0.40437827674463034 22.043712690887116 chr22 51304566 22252984 0.43374275888036945 16.75941848597401 chrMT 16571 11698 0.7059320499668095 1.0640012495633504 chrX 155270560 66418178 0.42775770242601047 20.192241938028733 chrY 59373566 3607917 0.060766385498893564 3.1402694584508604