BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777256.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 6,299,740 number of mapped reads = 6,172,188 (97.98%) number of supplementary alignments = 184,834 (2.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,100,427 number of mapped paired reads (second in pair) = 3,071,761 number of mapped paired reads (both in pair) = 6,132,188 number of mapped paired reads (singletons) = 40,000 number of mapped bases = 608,151,970 bp number of sequenced bases = 607,991,385 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 387,764 duplication rate = 4.71% >>>>>>> Insert size mean insert size = 104,059.9404 std insert size = 3,078,162.7058 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 53.1715 >>>>>>> ACTG content number of A's = 180,294,821 bp (29.65%) number of C's = 124,409,636 bp (20.46%) number of T's = 177,061,025 bp (29.12%) number of G's = 126,174,992 bp (20.75%) number of N's = 50,911 bp (0.01%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,822,424 number of insertions = 148,327 mapped reads with insertion percentage = 2.36% number of deletions = 69,767 mapped reads with deletion percentage = 1.11% homopolymer indels = 48.98% >>>>>>> Coverage mean coverageData = 0.1965X std coverageData = 1.8651X There is a 12.56% of reference with a coverageData >= 1X There is a 4.55% of reference with a coverageData >= 2X There is a 1.24% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% 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% 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 51801831 0.2078302986454746 4.584547417314445 chr2 243199373 59895798 0.24628269909232045 1.3604168902729257 chr3 198022430 39794077 0.200957421843576 0.663972039520356 chr4 191154276 37364815 0.19546941759231168 0.8468156622772334 chr5 180915260 40040764 0.22132330904535086 0.6317643669079681 chr6 171115067 28774142 0.1681566825439165 0.820427833399875 chr7 159138663 41678355 0.26189961769378445 1.7406930815901138 chr8 146364022 29909885 0.20435271312782044 0.9963224458628731 chr9 141213431 21950289 0.1554405189687658 1.7724606203755873 chr10 135534747 29787879 0.21978038591092808 3.4237508509341437 chr11 135006516 35255202 0.26113704022996936 1.0819975988301163 chr12 133851895 27463678 0.20517959794293536 0.6087257608344087 chr13 115169878 25439577 0.22088741814938798 0.6277027843748306 chr14 107349540 11865696 0.11053327289525414 0.45237933941483055 chr15 102531392 21258708 0.2073385290623968 0.6156163781413925 chr16 90354753 17351911 0.1920420390059613 1.6723101217031302 chr17 81195210 14302159 0.17614535389464478 0.8814847034970941 chr18 78077248 13375087 0.17130582010267575 1.9828728939178302 chr19 59128983 11518986 0.19481116392615783 2.555228335281445 chr20 63025520 15364753 0.24378621548858304 0.6872638668491674 chr21 48129895 5534692 0.11499489038985021 0.5565427134342431 chr22 51304566 4513847 0.08798138941473552 0.39791903633514125 chrMT 16571 2854581 172.2636533703458 43.4092630434187 chrX 155270560 19826716 0.12769140524771727 0.5964266165079879 chrY 59373566 1228542 0.02069173342224383 0.908343679516117