BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038482.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 15,033,856 number of mapped reads = 14,652,728 (97.46%) number of supplementary alignments = 265,237 (1.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,400,673 number of mapped paired reads (second in pair) = 7,252,055 number of mapped paired reads (both in pair) = 14,483,340 number of mapped paired reads (singletons) = 169,388 number of mapped bases = 2,105,170,712 bp number of sequenced bases = 2,103,528,443 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,473,872 duplication rate = 10.11% >>>>>>> Insert size mean insert size = 80,427.2925 std insert size = 2,657,624.6202 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 53.6542 >>>>>>> ACTG content number of A's = 625,000,191 bp (29.71%) number of C's = 421,222,038 bp (20.02%) number of T's = 624,626,683 bp (29.69%) number of G's = 432,634,340 bp (20.57%) number of N's = 45,191 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 30,530,106 number of insertions = 433,255 mapped reads with insertion percentage = 2.74% number of deletions = 798,689 mapped reads with deletion percentage = 5.21% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.68X std coverageData = 10.8227X There is a 25.62% of reference with a coverageData >= 1X There is a 14.52% of reference with a coverageData >= 2X There is a 8.07% of reference with a coverageData >= 3X There is a 4.99% of reference with a coverageData >= 4X There is a 3.06% of reference with a coverageData >= 5X There is a 1.96% of reference with a coverageData >= 6X There is a 1.27% of reference with a coverageData >= 7X There is a 0.85% of reference with a coverageData >= 8X There is a 0.58% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133910693 0.5372531970542211 9.723874746890427 chr2 243199373 191963205 0.7893244239572936 14.086073029935996 chr3 198022430 140281760 0.7084134862904167 1.6661196670784386 chr4 191154276 114383845 0.5983849662876493 10.412613240760836 chr5 180915260 125226951 0.6921856730051407 1.785634694601852 chr6 171115067 161054271 0.9412044995429888 15.90200640713644 chr7 159138663 156343236 0.9824340173072837 11.98045116483769 chr8 146364022 85740716 0.585804590693743 3.099149471024125 chr9 141213431 89096931 0.6309380798204669 18.356273794250804 chr10 135534747 91158932 0.6725871705799547 22.495583084683158 chr11 135006516 105463681 0.7811747471507227 7.385652812091835 chr12 133851895 66925191 0.4999943482309309 1.4210982571192468 chr13 115169878 127767724 1.1093849035769578 2.198279061606314 chr14 107349540 39504760 0.3680012042902093 1.4189221792978128 chr15 102531392 37214454 0.362956683549171 1.0895432845360726 chr16 90354753 85122979 0.942097412407292 17.722692185393406 chr17 81195210 47101911 0.5801070161651162 6.743958275394981 chr18 78077248 35708316 0.4573459863749296 15.7002458816843 chr19 59128983 27364187 0.4627880543793557 5.866125143182101 chr20 63025520 63617464 1.0093921319490897 3.5721436858361892 chr21 48129895 19854592 0.41252099137137116 5.138692467361559 chr22 51304566 11592049 0.22594575695270475 1.121015513098414 chrMT 16571 4619113 278.74678655482467 174.19924328614348 chrX 155270560 109940376 0.708056800980173 2.4818186309513237 chrY 59373566 34213375 0.5762391802439489 17.58227878000214