BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617670.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,536,755 (92.3%) number of supplementary alignments = 167,602 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,979,571 number of mapped paired reads (second in pair) = 14,557,184 number of mapped paired reads (both in pair) = 28,682,340 number of mapped paired reads (singletons) = 854,415 number of mapped bases = 2,848,000,541 bp number of sequenced bases = 2,846,290,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,649,257 duplication rate = 10.53% >>>>>>> Insert size mean insert size = 43,116.0241 std insert size = 1,924,622.1718 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.4603 >>>>>>> ACTG content number of A's = 848,891,870 bp (29.82%) number of C's = 564,648,397 bp (19.84%) number of T's = 846,779,777 bp (29.75%) number of G's = 581,092,443 bp (20.42%) number of N's = 4,878,362 bp (0.17%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0166 number of mismatches = 46,420,590 number of insertions = 444,720 mapped reads with insertion percentage = 1.48% number of deletions = 1,035,923 mapped reads with deletion percentage = 3.43% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.92X std coverageData = 10.2605X There is a 32.85% of reference with a coverageData >= 1X There is a 18.83% of reference with a coverageData >= 2X There is a 11.39% of reference with a coverageData >= 3X There is a 7.22% of reference with a coverageData >= 4X There is a 4.71% of reference with a coverageData >= 5X There is a 3.17% of reference with a coverageData >= 6X There is a 2.19% of reference with a coverageData >= 7X There is a 1.54% of reference with a coverageData >= 8X There is a 1.11% of reference with a coverageData >= 9X There is a 0.82% of reference with a coverageData >= 10X There is a 0.61% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% 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 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 174405908 0.6997210570640865 9.977571491919992 chr2 243199373 294469086 1.2108135081417335 11.689592109064955 chr3 198022430 239008097 1.206974871482993 2.4445997982404086 chr4 191154276 159692672 0.8354125020985667 7.97466877358261 chr5 180915260 188494543 1.0418941055608024 2.2814940746522687 chr6 171115067 138213618 0.8077232497591811 5.620347129071502 chr7 159138663 223157574 1.4022838309254866 13.166539831415205 chr8 146364022 126652016 0.8653220529837585 4.023997499976876 chr9 141213431 116626732 0.8258897979753781 19.558025378070717 chr10 135534747 120416202 0.8884526268381937 20.953875566370634 chr11 135006516 156249492 1.157347783124779 11.533601847816465 chr12 133851895 121581919 0.908331697507906 2.2355783993610334 chr13 115169878 122495551 1.0636075432848857 2.283183831695821 chr14 107349540 81416623 0.7584254483065321 2.4480918721239258 chr15 102531392 61003617 0.5949750199431604 1.7598905437028358 chr16 90354753 79099916 0.8754372445686394 16.46301343812868 chr17 81195210 69631714 0.8575840126529631 12.301966661645501 chr18 78077248 52581986 0.6734610574389097 17.701257623319318 chr19 59128983 30016405 0.5076428424280526 5.797818973797956 chr20 63025520 76616858 1.2156481691860694 2.959418314307979 chr21 48129895 41561078 0.8635189833678216 4.155487025156645 chr22 51304566 18238834 0.35550118482631743 1.2680058038397863 chrMT 16571 3015757 181.99004284593568 127.83660514079105 chrX 155270560 141939750 0.9141446388806739 4.244932179196308 chrY 59373566 11414593 0.1922504199933014 16.42122958937491