BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081955.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 = 2,941,741 number of mapped reads = 2,747,877 (93.41%) number of supplementary alignments = 18,653 (0.63%) number of secondary alignments = 0 number of mapped bases = 189,492,167 bp number of sequenced bases = 189,424,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,687 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7598 >>>>>>> ACTG content number of A's = 54,012,143 bp (28.51%) number of C's = 35,421,194 bp (18.7%) number of T's = 59,600,058 bp (31.46%) number of G's = 40,366,664 bp (21.31%) number of N's = 24,937 bp (0.01%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,416,401 number of insertions = 13,580 mapped reads with insertion percentage = 0.49% number of deletions = 38,091 mapped reads with deletion percentage = 1.37% homopolymer indels = 48.06% >>>>>>> Coverage mean coverageData = 0.0612X std coverageData = 0.5289X There is a 5.12% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17070513 0.06848734390916522 0.8884576503570815 chr2 243199373 16273409 0.06691386083466588 0.7225330732925277 chr3 198022430 11843299 0.059807866209903596 0.28405028595041254 chr4 191154276 9434822 0.04935710671729886 0.2820516145378341 chr5 180915260 10749019 0.05941466186987211 0.2825826760390377 chr6 171115067 16516334 0.09652179839896857 0.4754789451322651 chr7 159138663 12135580 0.07625789843414733 0.6882761833890935 chr8 146364022 10621903 0.07257181686357321 0.7554817017445504 chr9 141213431 11175692 0.0791404324706196 0.6204035980321803 chr10 135534747 7419483 0.054742294239867505 0.5387801854455504 chr11 135006516 8397388 0.06219987189359068 0.41140212175160557 chr12 133851895 7890035 0.05894600894518527 0.2980186912804884 chr13 115169878 5015967 0.04355276819864305 0.23617535569807113 chr14 107349540 4621039 0.04304665860701406 0.2944181095797621 chr15 102531392 4198489 0.04094832731813492 0.23511616003568928 chr16 90354753 4033275 0.04463821620983237 0.30747420837924727 chr17 81195210 5970272 0.07352985477837917 0.36338369661451875 chr18 78077248 5743580 0.07356278745890224 0.9158533585841901 chr19 59128983 2711619 0.045859388449146846 0.7267484734394967 chr20 63025520 4718129 0.0748606120187505 0.3204420154351582 chr21 48129895 1990859 0.041364291361948746 0.28645321697137355 chr22 51304566 1435387 0.02797776322676621 0.18705246787563218 chrMT 16571 128313 7.7432261179168425 4.38297835519219 chrX 155270560 8996919 0.05794349553450442 0.3321509991437746 chrY 59373566 400842 0.006751186209701469 0.17637745646662853