BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818992.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 = 2,075,549 number of mapped reads = 2,046,447 (98.6%) number of supplementary alignments = 28,968 (1.4%) number of secondary alignments = 0 number of mapped bases = 189,547,413 bp number of sequenced bases = 189,436,594 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 929,388 duplication rate = 37.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.142 >>>>>>> ACTG content number of A's = 53,233,567 bp (28.1%) number of C's = 39,762,581 bp (20.99%) number of T's = 54,189,734 bp (28.61%) number of G's = 42,241,528 bp (22.3%) number of N's = 9,184 bp (0%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,154,705 number of insertions = 25,360 mapped reads with insertion percentage = 1.21% number of deletions = 59,672 mapped reads with deletion percentage = 2.85% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.0612X std coverageData = 0.7063X There is a 2.78% of reference with a coverageData >= 1X There is a 1.35% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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% 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 19691199 0.07900160457373545 1.2267915515285024 chr2 243199373 14886734 0.06121205748338833 0.9245328479213133 chr3 198022430 9822537 0.04960315354174777 0.41764186787531854 chr4 191154276 10258718 0.053667216944704915 0.4915146684112666 chr5 180915260 10428455 0.057642760483554566 0.46440751336618274 chr6 171115067 7903316 0.04618714259685852 0.49229176618566733 chr7 159138663 9382713 0.058959355464737066 0.8084639864250047 chr8 146364022 17894299 0.12225886358875818 0.7302644202520828 chr9 141213431 8304627 0.05880904487052652 0.6965658903705759 chr10 135534747 9737528 0.07184525160916853 0.8420566891493344 chr11 135006516 5957136 0.04412480357614739 0.47731132267665877 chr12 133851895 8343177 0.06233140741115395 0.47826773855363386 chr13 115169878 4160604 0.03612580018535749 0.3515141582253402 chr14 107349540 4439771 0.04135808127356671 0.3977163205949666 chr15 102531392 4870484 0.04750236883548797 0.4187360328713169 chr16 90354753 5967645 0.06604682987733916 0.7992822251306452 chr17 81195210 6783665 0.08354760089911707 0.6243595042341875 chr18 78077248 4548210 0.05825269353755911 0.8291854212893375 chr19 59128983 4044646 0.06840378093430087 1.1337006718374334 chr20 63025520 5451208 0.08649207495630341 0.6033906031860045 chr21 48129895 2712821 0.05636457341118239 0.4871613789176262 chr22 51304566 1548936 0.030190997035234642 0.3662310148682241 chrMT 16571 142596 8.605153581558143 7.581731295035283 chrX 155270560 11583173 0.07459993059856292 0.6014977476787868 chrY 59373566 683215 0.01150705686096065 0.6245178960206947