BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238634.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,010,214 number of mapped reads = 1,676,722 (83.41%) number of supplementary alignments = 16,981 (0.84%) number of secondary alignments = 0 number of mapped bases = 101,610,146 bp number of sequenced bases = 101,551,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 720,981 duplication rate = 23.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4031 >>>>>>> ACTG content number of A's = 25,464,383 bp (25.08%) number of C's = 16,719,606 bp (16.46%) number of T's = 35,803,361 bp (35.26%) number of G's = 23,561,864 bp (23.2%) number of N's = 2,101 bp (0%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 653,108 number of insertions = 7,008 mapped reads with insertion percentage = 0.41% number of deletions = 35,003 mapped reads with deletion percentage = 2.06% homopolymer indels = 41.08% >>>>>>> Coverage mean coverageData = 0.0328X std coverageData = 0.8303X There is a 0.91% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 8582897 0.03443480688459348 0.5614297045042486 chr2 243199373 16893021 0.06946161411361862 1.673513431574315 chr3 198022430 10719184 0.054131160798299466 0.6870319702513377 chr4 191154276 4073002 0.0213074072169853 0.40059240380079514 chr5 180915260 4137537 0.022870027658252818 0.42243596300910063 chr6 171115067 10396850 0.060759407001839294 0.8989603011313414 chr7 159138663 3386135 0.021277890213266402 0.5550594845214544 chr8 146364022 4614336 0.0315264361893526 0.6470023915315717 chr9 141213431 2009064 0.01422714529186675 0.3439292962644299 chr10 135534747 2932407 0.021635831880071316 0.43036162086111324 chr11 135006516 4087272 0.030274627633528443 0.5123678234602594 chr12 133851895 3350073 0.025028207482606056 0.45168079321104726 chr13 115169878 2788435 0.024211495648193707 0.5986313970510434 chr14 107349540 1964004 0.01829541141955522 0.38389802244171206 chr15 102531392 959053 0.009353749922755365 0.4048403197783814 chr16 90354753 1989910 0.022023301862161032 0.4322454694601261 chr17 81195210 1388100 0.017095836072103267 0.3713015546392315 chr18 78077248 3853521 0.0493552359837273 2.8754479613646504 chr19 59128983 1287881 0.02178087520970892 0.4628231034300203 chr20 63025520 2344535 0.03719977240965247 0.5497821453997839 chr21 48129895 2937255 0.061027662744745234 0.716193797323011 chr22 51304566 773833 0.015083121451607251 0.3352258243036784 chrMT 16571 80558 4.861384346146883 8.67690581221043 chrX 155270560 5788809 0.03728207716903964 0.5580636873642411 chrY 59373566 272474 0.004589146624610689 0.27518651966948027