BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084870.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 = 2,478,173 number of mapped reads = 2,216,419 (89.44%) number of supplementary alignments = 16,046 (0.65%) number of secondary alignments = 0 number of mapped bases = 153,743,266 bp number of sequenced bases = 153,682,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,298 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7311 >>>>>>> ACTG content number of A's = 44,709,146 bp (29.09%) number of C's = 28,323,075 bp (18.43%) number of T's = 49,088,123 bp (31.94%) number of G's = 31,537,715 bp (20.52%) number of N's = 24,086 bp (0.02%) GC percentage = 38.95% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,293,795 number of insertions = 12,676 mapped reads with insertion percentage = 0.57% number of deletions = 34,443 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.61% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.4573X There is a 4.17% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 15153516 0.060796301887649055 1.0196061039758784 chr2 243199373 12692267 0.05218873241091785 0.43810343807334134 chr3 198022430 6417751 0.03240921243113722 0.20880088089234614 chr4 191154276 6629997 0.03468401093993838 0.23099331486054328 chr5 180915260 6262036 0.03461308902300447 0.22543213286343597 chr6 171115067 8792108 0.05138126147594005 0.2635044665789875 chr7 159138663 7845934 0.04930250042379707 0.4089664887825899 chr8 146364022 8100994 0.05534826038054625 0.7388994925119531 chr9 141213431 13276492 0.09401720435501634 0.4756306321974754 chr10 135534747 6953651 0.05130530106792467 0.36423482922293604 chr11 135006516 7000855 0.0518556822842536 0.3197714135638731 chr12 133851895 7126898 0.053244655221354915 0.26882411740063156 chr13 115169878 4021373 0.0349168816519889 0.21001633709830986 chr14 107349540 3959311 0.03688242166664152 0.2336032651394482 chr15 102531392 5210544 0.05081901160573339 0.25600570318700894 chr16 90354753 3600751 0.03985126272217246 0.2639745716091707 chr17 81195210 4363948 0.05374637247689858 0.27579225325800655 chr18 78077248 5617714 0.07195071732036457 0.7440120059783422 chr19 59128983 3795454 0.0641894009913886 0.5530438283126495 chr20 63025520 2768439 0.04392568280277576 0.25082631401535704 chr21 48129895 2222052 0.04616781316477005 0.27046013775686023 chr22 51304566 1537993 0.02997770217956819 0.1933984581512174 chrMT 16571 226465 13.666344819262568 6.8723963007764866 chrX 155270560 9802368 0.06313088585498758 0.3089772726249566 chrY 59373566 364355 0.006136653473028721 0.16614156215696552