BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054596.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 4,495,535 number of mapped reads = 3,426,504 (76.22%) number of supplementary alignments = 93 (0%) number of secondary alignments = 0 number of mapped bases = 159,763,702 bp number of sequenced bases = 159,731,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 615,611 duplication rate = 13.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.587 >>>>>>> ACTG content number of A's = 48,703,946 bp (30.49%) number of C's = 32,098,001 bp (20.09%) number of T's = 46,827,295 bp (29.32%) number of G's = 32,100,364 bp (20.1%) number of N's = 1,745 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,053,973 number of insertions = 6,942 mapped reads with insertion percentage = 0.2% number of deletions = 22,135 mapped reads with deletion percentage = 0.64% homopolymer indels = 44.65% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.4604X There is a 2.81% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% 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 0.02% 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% 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 14618458 0.05864963521996601 0.5166928188328225 chr2 243199373 13086064 0.05380796767103507 0.49749719526927955 chr3 198022430 11595479 0.058556391818845976 0.46616824505049514 chr4 191154276 7666252 0.04010505106357129 0.38696644619020587 chr5 180915260 8171851 0.045169495375901404 0.39706952642713955 chr6 171115067 8183182 0.047822685304503315 0.45076970641836334 chr7 159138663 9577362 0.06018249631769245 0.5072802972112792 chr8 146364022 8960036 0.0612174759723397 0.5048585489933125 chr9 141213431 7974142 0.05646872215717215 0.4806620185410951 chr10 135534747 6956400 0.051325583689620195 0.44479432580640327 chr11 135006516 6119716 0.045329041747881264 0.439990146017619 chr12 133851895 6106184 0.04561895817761863 0.3975204033903206 chr13 115169878 4961180 0.043077062215868635 0.39128386175967317 chr14 107349540 3762524 0.03504927920510884 0.381324028226941 chr15 102531392 4316291 0.04209726324597251 0.37905962046036107 chr16 90354753 4619575 0.05112708348613382 0.4641872826475272 chr17 81195210 3081266 0.037948864224872376 0.3572146573299169 chr18 78077248 7020917 0.08992270065666248 0.6463197488225562 chr19 59128983 2625722 0.04440668292908065 0.4567794157751696 chr20 63025520 3145122 0.049902357013476444 0.4278915119918251 chr21 48129895 2092088 0.043467537172063225 0.4391788771511129 chr22 51304566 2053957 0.04003458483597737 0.3711383725319573 chrMT 16571 17560 1.0596825779977068 2.1123756929468804 chrX 155270560 12616413 0.08125437945222842 0.6049921067654257 chrY 59373566 435961 0.007342678389908398 0.15646058437565968