BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818961.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,467,680 number of mapped reads = 1,438,714 (98.03%) number of supplementary alignments = 26,495 (1.81%) number of secondary alignments = 0 number of mapped bases = 132,360,582 bp number of sequenced bases = 132,260,096 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 702,436 duplication rate = 39.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0334 >>>>>>> ACTG content number of A's = 37,623,602 bp (28.45%) number of C's = 29,273,949 bp (22.13%) number of T's = 37,942,188 bp (28.69%) number of G's = 27,414,515 bp (20.73%) number of N's = 5,842 bp (0%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 986,526 number of insertions = 18,802 mapped reads with insertion percentage = 1.25% number of deletions = 52,527 mapped reads with deletion percentage = 3.56% homopolymer indels = 41.25% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.6448X There is a 1.81% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 15702752 0.06299985106155463 0.9708220354330959 chr2 243199373 11997464 0.049331804815138235 1.1656037464888198 chr3 198022430 8587763 0.04336762759653035 0.4098217853857934 chr4 191154276 8740255 0.045723565189826045 0.47685122304465744 chr5 180915260 6752937 0.03732651960923584 0.4023293053283384 chr6 171115067 7188355 0.04200889568654992 0.4543353561652973 chr7 159138663 6537155 0.04107835818628186 0.4682232082611956 chr8 146364022 8730629 0.059650103083393 0.5618793412153817 chr9 141213431 4895122 0.03466470551232482 0.6127156329962544 chr10 135534747 6484808 0.04784609219066163 0.8045763875784859 chr11 135006516 4970246 0.0368148601064559 0.4375787641668876 chr12 133851895 5982872 0.04469770114199728 0.4299828451367044 chr13 115169878 2118105 0.018391136960308318 0.2609869257761589 chr14 107349540 3218999 0.02998614619121796 0.3852940154257873 chr15 102531392 3771804 0.036786821347358674 0.37899565518547124 chr16 90354753 4054186 0.04486964841794211 0.8564792414575134 chr17 81195210 2721715 0.03352063502268176 0.3996114048645323 chr18 78077248 3392899 0.04345566841700158 0.7278519323855441 chr19 59128983 2034385 0.03440588518155301 0.7750014251580293 chr20 63025520 2844086 0.04512594263403142 0.4543783463887288 chr21 48129895 1816565 0.037742966195957836 0.4127549229894198 chr22 51304566 1607340 0.031329375245080525 0.39371951563256274 chrMT 16571 112670 6.799227566230162 5.976937213615865 chrX 155270560 7561621 0.04869964402781828 0.5034492912313153 chrY 59373566 535849 0.009025043232202021 0.8539427036450774