BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081256.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 = 3,227,156 number of mapped reads = 2,632,838 (81.58%) number of supplementary alignments = 21,923 (0.68%) number of secondary alignments = 0 number of mapped bases = 176,589,414 bp number of sequenced bases = 176,522,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,100 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3875 >>>>>>> ACTG content number of A's = 48,789,716 bp (27.64%) number of C's = 31,787,000 bp (18.01%) number of T's = 57,090,449 bp (32.34%) number of G's = 38,810,634 bp (21.99%) number of N's = 44,756 bp (0.03%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,526,876 number of insertions = 14,984 mapped reads with insertion percentage = 0.56% number of deletions = 41,060 mapped reads with deletion percentage = 1.54% homopolymer indels = 49.37% >>>>>>> Coverage mean coverageData = 0.057X std coverageData = 0.4643X There is a 4.64% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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% 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 14204724 0.05698972360835161 0.8481299540700548 chr2 243199373 14693489 0.06041746250719158 0.4665477161873425 chr3 198022430 12139895 0.061305656131984645 0.2922950069706744 chr4 191154276 11742034 0.06142700150741069 0.3171461069976236 chr5 180915260 10819776 0.0598057676284466 0.2902154407776548 chr6 171115067 10334889 0.06039730563293997 0.3635692071099834 chr7 159138663 10502513 0.06599598615453996 0.6621022280599844 chr8 146364022 8827184 0.060309793891834974 0.648449196993929 chr9 141213431 7302913 0.05171542783348986 0.4243148279423113 chr10 135534747 8140988 0.06006568928040276 0.44825652028227153 chr11 135006516 8056753 0.059676771453016385 0.4174449041469307 chr12 133851895 8194627 0.06122159869309284 0.2976984405962478 chr13 115169878 5662778 0.049168915504104294 0.26128504485498805 chr14 107349540 5456603 0.05083024109837825 0.28598702424856176 chr15 102531392 4980632 0.048576654455252104 0.2572309953742529 chr16 90354753 4665657 0.05163709539441716 0.2974145020764379 chr17 81195210 3894216 0.047961154358736185 0.30129442887297425 chr18 78077248 5183332 0.066387227172761 0.7899495753785037 chr19 59128983 3208336 0.05425995573101604 0.6165195001246733 chr20 63025520 3613102 0.05732760316773269 0.2892023760999963 chr21 48129895 2436849 0.05063067351383169 0.2983583784732026 chr22 51304566 1646363 0.03208998980714504 0.20793683232515484 chrMT 16571 25528 1.5405225997224066 1.5794257992710825 chrX 155270560 10417884 0.06709503720473475 0.3387436284599529 chrY 59373566 438349 0.007382898308651362 0.1747239309853768