BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090144.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 = 27,593,939 number of mapped reads = 24,640,873 (89.3%) number of supplementary alignments = 176,720 (0.64%) number of secondary alignments = 0 number of mapped bases = 1,633,473,968 bp number of sequenced bases = 1,632,844,034 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,731,849 duplication rate = 7.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.887 >>>>>>> ACTG content number of A's = 454,367,785 bp (27.83%) number of C's = 306,057,278 bp (18.74%) number of T's = 503,402,471 bp (30.83%) number of G's = 368,049,141 bp (22.54%) number of N's = 967,359 bp (0.06%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 13,196,510 number of insertions = 115,299 mapped reads with insertion percentage = 0.46% number of deletions = 373,899 mapped reads with deletion percentage = 1.5% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.5277X std coverageData = 4.5239X There is a 25.7% of reference with a coverageData >= 1X There is a 11.82% of reference with a coverageData >= 2X There is a 5.88% of reference with a coverageData >= 3X There is a 3.11% of reference with a coverageData >= 4X There is a 1.75% of reference with a coverageData >= 5X There is a 1.03% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 137664693 0.552314343080413 8.278750374453494 chr2 243199373 145004456 0.5962369648050039 6.434742576778866 chr3 198022430 152978653 0.772531944992292 1.6593309888509162 chr4 191154276 85569900 0.4476483696341692 1.5323647624274572 chr5 180915260 74775547 0.4133180749926789 1.1959251079367006 chr6 171115067 91690645 0.5358420307897258 2.0216768589585157 chr7 159138663 122978030 0.7727727987761214 9.30933260172829 chr8 146364022 154226324 1.0537174497705455 7.015660691306114 chr9 141213431 52061499 0.368672431732078 4.360394414572526 chr10 135534747 50891805 0.3754889880747702 3.2506725373043346 chr11 135006516 68471985 0.5071754092224704 3.6356427064357812 chr12 133851895 59352847 0.44342179092795064 1.348783153888845 chr13 115169878 50589969 0.4392638932898757 1.110756382047172 chr14 107349540 57796022 0.5383909609673223 1.623822666855325 chr15 102531392 42031657 0.4099393969019752 1.18830618058251 chr16 90354753 32224396 0.3566430644771947 1.3910469355846582 chr17 81195210 32313641 0.3979747204299367 1.752013791530235 chr18 78077248 62906928 0.8057011435648962 6.354828333609363 chr19 59128983 26281879 0.4444838667358781 4.961762072303552 chr20 63025520 39199076 0.6219556141702599 1.6621657130298748 chr21 48129895 24940954 0.5182008811779041 1.6111704057382317 chr22 51304566 12752691 0.24856834380004306 0.8161524900712951 chrMT 16571 967377 58.37770804417356 31.651182201323305 chrX 155270560 51973931 0.334731394026015 1.926730086635487 chrY 59373566 3829063 0.06449103966569904 2.647807606408171