BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818834.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,203,983 number of mapped reads = 2,176,649 (98.76%) number of supplementary alignments = 34,792 (1.58%) number of secondary alignments = 0 number of mapped bases = 201,583,547 bp number of sequenced bases = 201,460,339 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 557,238 duplication rate = 21.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.334 >>>>>>> ACTG content number of A's = 57,023,322 bp (28.3%) number of C's = 43,305,479 bp (21.5%) number of T's = 57,313,774 bp (28.45%) number of G's = 43,814,844 bp (21.75%) number of N's = 2,920 bp (0%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,180,291 number of insertions = 28,464 mapped reads with insertion percentage = 1.27% number of deletions = 63,681 mapped reads with deletion percentage = 2.86% homopolymer indels = 40.26% >>>>>>> Coverage mean coverageData = 0.0651X std coverageData = 0.7247X There is a 4.23% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 18396828 0.07380855432251862 1.1539477701445677 chr2 243199373 14654376 0.060256635612296584 1.0431639065767486 chr3 198022430 11797990 0.05957905879652118 0.34417197998889926 chr4 191154276 11719902 0.06131122068124702 0.43638702832615506 chr5 180915260 10562692 0.058384748749221047 0.35533413994098423 chr6 171115067 9569063 0.055921802607832305 0.37248324220819606 chr7 159138663 17167632 0.10787844811791589 1.4251426734083161 chr8 146364022 19281462 0.13173634979776655 0.6580794069428882 chr9 141213431 7083297 0.050160221657669375 0.5984252367159264 chr10 135534747 7994045 0.05898151711604995 0.8977814785587507 chr11 135006516 8577061 0.06353071876915926 0.44355971309915804 chr12 133851895 7499165 0.05602584109847679 0.33709850255033436 chr13 115169878 4899085 0.04253790214139152 0.28965118310161797 chr14 107349540 6516119 0.060700017904128885 0.37798941321936697 chr15 102531392 5370119 0.05237536422016001 0.33309015569230604 chr16 90354753 4800048 0.05312446595919531 0.7661973728961785 chr17 81195210 5282419 0.06505825897857767 0.4817834918086659 chr18 78077248 3443429 0.04410284798972423 0.7207641156695703 chr19 59128983 3872408 0.06549086088627637 1.0966836522384167 chr20 63025520 8062386 0.127922562162121 0.5483806465150632 chr21 48129895 2391908 0.04969692952789529 0.3696882485732713 chr22 51304566 2424377 0.0472546049799934 0.3439242298529683 chrMT 16571 358114 21.610886488443665 14.050587732657613 chrX 155270560 9143262 0.05888599873665684 0.41440422029298885 chrY 59373566 716360 0.012065301922407692 0.8614233590959764