BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089695.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 = 19,811,324 number of mapped reads = 14,382,590 (72.6%) number of supplementary alignments = 595 (0%) number of secondary alignments = 0 number of mapped bases = 665,941,815 bp number of sequenced bases = 665,806,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,124,725 duplication rate = 5.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7242 >>>>>>> ACTG content number of A's = 208,414,289 bp (31.3%) number of C's = 136,538,602 bp (20.51%) number of T's = 179,643,918 bp (26.98%) number of G's = 140,918,120 bp (21.17%) number of N's = 291,862 bp (0.04%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 5,190,346 number of insertions = 32,513 mapped reads with insertion percentage = 0.23% number of deletions = 91,993 mapped reads with deletion percentage = 0.64% homopolymer indels = 42.96% >>>>>>> Coverage mean coverageData = 0.2151X std coverageData = 1.146X There is a 13.03% of reference with a coverageData >= 1X There is a 4.31% of reference with a coverageData >= 2X There is a 1.78% of reference with a coverageData >= 3X There is a 0.85% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% 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 53005221 0.21265833074895327 1.3076716342075128 chr2 243199373 64534542 0.2653565311617806 1.748898281323942 chr3 198022430 62781806 0.3170439126517132 0.9617792798256549 chr4 191154276 27467289 0.1436917320123145 0.5999877443196376 chr5 180915260 28792642 0.1591498804467904 0.6194515707484692 chr6 171115067 40702730 0.2378675981817545 0.9256017845001699 chr7 159138663 45426500 0.2854523165121728 1.8814114429778623 chr8 146364022 54440864 0.3719552336434155 2.0806646842543266 chr9 141213431 24024613 0.17012980160506122 1.012077097447022 chr10 135534747 27087389 0.19985567981323638 1.0233118955540788 chr11 135006516 31965889 0.23677293472264702 1.0244478556003296 chr12 133851895 19345751 0.14453102064785858 0.6154989931380256 chr13 115169878 21474924 0.18646302638264495 0.681806547837323 chr14 107349540 22317299 0.20789375529694865 0.7963996961283111 chr15 102531392 16866476 0.16450060484890325 0.626790816088755 chr16 90354753 13503355 0.1494481978164447 0.6659963962583031 chr17 81195210 15760219 0.19410281714894265 0.7758522818803139 chr18 78077248 32744867 0.4193906398955045 1.5568195979661674 chr19 59128983 10240649 0.1731916985617696 1.2643796425505003 chr20 63025520 15052053 0.23882473321917852 0.8070934498674768 chr21 48129895 10733424 0.2230095037606045 0.8326637747796352 chr22 51304566 5134722 0.10008313879899111 0.4797496297102859 chrMT 16571 15306 0.9236618188401424 2.2772912790983657 chrX 155270560 21003349 0.13526935820930897 0.8249150943155206 chrY 59373566 1519936 0.02559954037458353 0.3493522212079425