BamQC report ----------------------------------- >>>>>>> Input bam file = SRR052148.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 = 11,305,884 number of mapped reads = 7,093,758 (62.74%) number of supplementary alignments = 148 (0%) number of secondary alignments = 0 number of mapped bases = 326,324,153 bp number of sequenced bases = 326,263,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,831,239 duplication rate = 18.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1409 >>>>>>> ACTG content number of A's = 96,557,870 bp (29.6%) number of C's = 66,812,672 bp (20.48%) number of T's = 96,086,992 bp (29.45%) number of G's = 66,644,053 bp (20.43%) number of N's = 162,317 bp (0.05%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 4,831,769 number of insertions = 18,299 mapped reads with insertion percentage = 0.26% number of deletions = 42,356 mapped reads with deletion percentage = 0.59% homopolymer indels = 37.7% >>>>>>> Coverage mean coverageData = 0.1054X std coverageData = 0.8911X There is a 4.22% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% 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 0.01% 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% 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 25608001 0.10273996870001781 0.9597863758333699 chr2 243199373 27926179 0.11482833469311617 0.9706362495498105 chr3 198022430 22246455 0.11234310678845826 0.859189606470921 chr4 191154276 21343284 0.11165475576387315 0.8794553264713378 chr5 180915260 20347146 0.11246782609714626 0.8570567101997906 chr6 171115067 19430543 0.11355249622758234 0.9502036972251038 chr7 159138663 17881611 0.1123649694103563 0.9975546584585245 chr8 146364022 16808365 0.11483945829255772 0.9675971638470634 chr9 141213431 13392211 0.09483666606754991 0.8120392018503866 chr10 135534747 15078496 0.11125188435995678 0.9000749332206445 chr11 135006516 14936541 0.1106357044277774 0.9739382338846666 chr12 133851895 15053709 0.11246541559983143 0.863336127151809 chr13 115169878 10497057 0.09114411842999434 0.7761183811074692 chr14 107349540 9988749 0.09304882908673852 0.8514403126986749 chr15 102531392 9384679 0.09152981166977622 0.7532064053086981 chr16 90354753 9107319 0.1007951291726734 0.8146553625397982 chr17 81195210 8336601 0.10267355672828483 0.7960827438744266 chr18 78077248 8403345 0.10762860135644126 0.9263381920616104 chr19 59128983 5910751 0.09996368447602083 0.9494227499440183 chr20 63025520 6883284 0.10921423575719803 0.8457205198802619 chr21 48129895 4130590 0.08582171226427981 0.7718900340883814 chr22 51304566 3434676 0.06694678988221048 0.6307359388746319 chrMT 16571 208221 12.565385311689095 20.327791171225783 chrX 155270560 19088367 0.12293616381624436 0.9675068273659094 chrY 59373566 897973 0.015124121060877495 0.2952859010778834