BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472797.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 = 58,394,144 number of mapped reads = 58,022,155 (99.36%) number of supplementary alignments = 70,605 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,150,727 number of mapped paired reads (second in pair) = 28,871,428 number of mapped paired reads (both in pair) = 57,720,860 number of mapped paired reads (singletons) = 301,295 number of mapped bases = 5,739,696,118 bp number of sequenced bases = 5,738,937,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,458,333 duplication rate = 38.52% >>>>>>> Insert size mean insert size = 20,844.6103 std insert size = 1,426,869.5362 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.6524 >>>>>>> ACTG content number of A's = 1,624,546,347 bp (28.31%) number of C's = 1,243,211,819 bp (21.66%) number of T's = 1,648,067,520 bp (28.72%) number of G's = 1,222,519,964 bp (21.3%) number of N's = 591,687 bp (0.01%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 26,208,979 number of insertions = 272,405 mapped reads with insertion percentage = 0.46% number of deletions = 322,146 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 1.8541X std coverageData = 12.6817X There is a 10.48% of reference with a coverageData >= 1X There is a 6.74% of reference with a coverageData >= 2X There is a 5.23% of reference with a coverageData >= 3X There is a 4.72% of reference with a coverageData >= 4X There is a 4.34% of reference with a coverageData >= 5X There is a 4.1% of reference with a coverageData >= 6X There is a 3.89% of reference with a coverageData >= 7X There is a 3.72% of reference with a coverageData >= 8X There is a 3.56% of reference with a coverageData >= 9X There is a 3.42% of reference with a coverageData >= 10X There is a 3.3% of reference with a coverageData >= 11X There is a 3.18% of reference with a coverageData >= 12X There is a 3.07% of reference with a coverageData >= 13X There is a 2.97% of reference with a coverageData >= 14X There is a 2.87% of reference with a coverageData >= 15X There is a 2.78% of reference with a coverageData >= 16X There is a 2.69% of reference with a coverageData >= 17X There is a 2.61% of reference with a coverageData >= 18X There is a 2.54% of reference with a coverageData >= 19X There is a 2.46% of reference with a coverageData >= 20X There is a 2.39% of reference with a coverageData >= 21X There is a 2.32% of reference with a coverageData >= 22X There is a 2.26% of reference with a coverageData >= 23X There is a 2.2% of reference with a coverageData >= 24X There is a 2.14% of reference with a coverageData >= 25X There is a 2.08% of reference with a coverageData >= 26X There is a 2.03% of reference with a coverageData >= 27X There is a 1.98% of reference with a coverageData >= 28X There is a 1.93% of reference with a coverageData >= 29X There is a 1.88% of reference with a coverageData >= 30X There is a 1.83% of reference with a coverageData >= 31X There is a 1.79% of reference with a coverageData >= 32X There is a 1.74% of reference with a coverageData >= 33X There is a 1.7% of reference with a coverageData >= 34X There is a 1.66% of reference with a coverageData >= 35X There is a 1.62% of reference with a coverageData >= 36X There is a 1.59% of reference with a coverageData >= 37X There is a 1.55% of reference with a coverageData >= 38X There is a 1.51% of reference with a coverageData >= 39X There is a 1.48% of reference with a coverageData >= 40X There is a 1.44% of reference with a coverageData >= 41X There is a 1.41% of reference with a coverageData >= 42X There is a 1.38% of reference with a coverageData >= 43X There is a 1.35% of reference with a coverageData >= 44X There is a 1.32% of reference with a coverageData >= 45X There is a 1.29% of reference with a coverageData >= 46X There is a 1.26% of reference with a coverageData >= 47X There is a 1.24% of reference with a coverageData >= 48X There is a 1.21% of reference with a coverageData >= 49X There is a 1.18% of reference with a coverageData >= 50X There is a 1.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 601198254 2.4120230938160834 15.221587816878003 chr2 243199373 515849654 2.1210977957578865 15.126504065292153 chr3 198022430 364291060 1.8396454381455676 12.477544476475046 chr4 191154276 252718500 1.3220656387513927 10.172720685070106 chr5 180915260 284910699 1.5748295583247096 11.363692080215936 chr6 171115067 312417499 1.8257743428286184 12.621146178088463 chr7 159138663 315386262 1.9818330508406998 13.89358723978849 chr8 146364022 211855255 1.447454450247343 10.91848674307558 chr9 141213431 245687958 1.739834208829612 12.537937521378428 chr10 135534747 262897614 1.9397063839282482 13.426239685654869 chr11 135006516 263361322 1.950730452150917 11.75581204538657 chr12 133851895 305554438 2.2827800682239126 13.332023082180045 chr13 115169878 159624334 1.3859903020822857 12.144415738518402 chr14 107349540 173892143 1.6198685434516067 11.525514139452886 chr15 102531392 197707398 1.9282621072773498 12.154375010443022 chr16 90354753 203523004 2.252488078850705 14.113851804933207 chr17 81195210 259356681 3.194236224033413 14.969216021814594 chr18 78077248 99906311 1.2795828946225154 10.152890735905347 chr19 59128983 217802699 3.683518436297137 15.81959594983943 chr20 63025520 142217756 2.256510632518383 13.891085245367606 chr21 48129895 66122109 1.37382616355178 11.959903583971771 chr22 51304566 88918937 1.7331583508571147 11.027019916741331 chrMT 16571 777705 46.93168788847987 131.47655933725653 chrX 155270560 165516215 1.06598581856084 8.4488873764016 chrY 59373566 28202311 0.474997762472276 7.117235538696039