BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089601.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 = 25,712,347 number of mapped reads = 20,076,263 (78.08%) number of supplementary alignments = 843 (0%) number of secondary alignments = 0 number of mapped bases = 924,077,869 bp number of sequenced bases = 923,896,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,891,813 duplication rate = 7.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5291 >>>>>>> ACTG content number of A's = 282,990,178 bp (30.63%) number of C's = 193,638,805 bp (20.96%) number of T's = 251,579,440 bp (27.23%) number of G's = 195,581,669 bp (21.17%) number of N's = 106,803 bp (0.01%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 4,075,494 number of insertions = 41,583 mapped reads with insertion percentage = 0.21% number of deletions = 121,699 mapped reads with deletion percentage = 0.6% homopolymer indels = 42.29% >>>>>>> Coverage mean coverageData = 0.2985X std coverageData = 1.5692X There is a 16.14% of reference with a coverageData >= 1X There is a 6.34% of reference with a coverageData >= 2X There is a 2.94% of reference with a coverageData >= 3X There is a 1.53% of reference with a coverageData >= 4X There is a 0.86% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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 0.01% 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% 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 73265233 0.293942027931798 2.436117243735658 chr2 243199373 78116378 0.32120304027264085 1.96049623337025 chr3 198022430 62787651 0.31707342950998024 0.9679801813871758 chr4 191154276 60317524 0.3155436815862806 1.0565129761533725 chr5 180915260 58006300 0.32062690565737795 0.992996214429483 chr6 171115067 54368460 0.3177304076911006 1.197133498779638 chr7 159138663 50291399 0.3160225054800165 2.178686089645841 chr8 146364022 46581950 0.3182609316379677 2.2877578272106933 chr9 141213431 38667328 0.27382188596494056 1.484577524641232 chr10 135534747 43640644 0.32198860414739255 1.5432981341533505 chr11 135006516 41930826 0.31058372027021275 1.5274018189638288 chr12 133851895 41880388 0.3128860297420518 1.037444410410935 chr13 115169878 30175657 0.2620099762543814 0.8862563602099305 chr14 107349540 28154571 0.2622700665508208 1.1682862563622156 chr15 102531392 25941264 0.25300801534031647 0.8726747190048594 chr16 90354753 25578176 0.283086115015997 1.0983550360982295 chr17 81195210 23680194 0.2916452091200947 1.154136969294039 chr18 78077248 24290249 0.31110534274978546 2.4320369763139227 chr19 59128983 17398606 0.29424835532855353 2.2024105225265154 chr20 63025520 19406818 0.3079199981213959 1.0770847806864305 chr21 48129895 11909816 0.24745152674860396 1.0738539440344925 chr22 51304566 10244963 0.19968910759326958 0.7835313677546322 chrMT 16571 27817 1.6786554824693742 2.5033704605453297 chrX 155270560 54751307 0.3526187256618383 1.3873925493969603 chrY 59373566 2664350 0.04487434694422767 0.6572563551775706