BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080683.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,253,538 number of mapped reads = 1,152,848 (91.97%) number of supplementary alignments = 12,450 (0.99%) number of secondary alignments = 0 number of mapped bases = 76,619,669 bp number of sequenced bases = 76,591,260 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,386 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9428 >>>>>>> ACTG content number of A's = 21,094,170 bp (27.54%) number of C's = 13,986,635 bp (18.26%) number of T's = 24,449,175 bp (31.92%) number of G's = 17,057,696 bp (22.27%) number of N's = 3,584 bp (0%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 513,555 number of insertions = 5,736 mapped reads with insertion percentage = 0.49% number of deletions = 17,449 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.9% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.2085X There is a 2.2% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 9377254 0.03762178791121246 0.2463563192724258 chr2 243199373 5100484 0.02097243893799019 0.29482175085587087 chr3 198022430 4592117 0.02318988308546663 0.16674395921801255 chr4 191154276 3247506 0.016988926787073286 0.14554436838786838 chr5 180915260 3366174 0.018606357473659216 0.14947489738006067 chr6 171115067 4551722 0.026600357758092687 0.21072694730505248 chr7 159138663 5932336 0.037277779567621475 0.3695720148203791 chr8 146364022 9092245 0.062120764896717584 0.3037257495307103 chr9 141213431 2331796 0.016512565295577302 0.15983576928306475 chr10 135534747 3583696 0.026441160509194 0.1853106492573423 chr11 135006516 3066635 0.022714718451070908 0.17694590138499355 chr12 133851895 2396053 0.01790077757210684 0.1474327463095125 chr13 115169878 1619510 0.014061923378958516 0.13110930572178206 chr14 107349540 1504907 0.014018755925735685 0.13085063655023152 chr15 102531392 1376189 0.013422123440984786 0.13342075999111366 chr16 90354753 1846361 0.020434575256931972 0.15854313652523047 chr17 81195210 1152689 0.014196514794407207 0.13198263567364663 chr18 78077248 2387436 0.030577870777412648 0.21919297919258693 chr19 59128983 1180411 0.01996332323185738 0.17593707612555934 chr20 63025520 1991354 0.03159599476529507 0.196397426965875 chr21 48129895 1148268 0.02385768761805942 0.17171677483439474 chr22 51304566 751186 0.014641698752504796 0.13120173193135684 chrMT 16571 12608 0.760847263291292 0.9884749450852741 chrX 155270560 4867663 0.03134955525374546 0.19890852708757742 chrY 59373566 143069 0.002409641354538146 0.05735655331963296