BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672005.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 215,837,844 number of mapped reads = 214,920,994 (99.58%) number of supplementary alignments = 861,478 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 107,469,316 number of mapped paired reads (second in pair) = 107,451,678 number of mapped paired reads (both in pair) = 214,601,436 number of mapped paired reads (singletons) = 319,558 number of mapped bases = 31,871,733,641 bp number of sequenced bases = 31,859,167,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,315,134 duplication rate = 26.57% >>>>>>> Insert size mean insert size = 43,785.3785 std insert size = 1,978,330.8724 median insert size = 380 >>>>>>> Mapping quality mean mapping quality = 54.4648 >>>>>>> ACTG content number of A's = 9,412,856,965 bp (29.55%) number of C's = 6,531,170,191 bp (20.5%) number of T's = 9,357,906,057 bp (29.37%) number of G's = 6,557,097,443 bp (20.58%) number of N's = 137,253 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 184,372,345 number of insertions = 4,320,396 mapped reads with insertion percentage = 1.91% number of deletions = 4,671,337 mapped reads with deletion percentage = 2.09% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 10.2955X std coverageData = 116.2834X There is a 91.49% of reference with a coverageData >= 1X There is a 91.09% of reference with a coverageData >= 2X There is a 90.18% of reference with a coverageData >= 3X There is a 88.43% of reference with a coverageData >= 4X There is a 85.5% of reference with a coverageData >= 5X There is a 81.18% of reference with a coverageData >= 6X There is a 75.45% of reference with a coverageData >= 7X There is a 68.46% of reference with a coverageData >= 8X There is a 60.58% of reference with a coverageData >= 9X There is a 52.24% of reference with a coverageData >= 10X There is a 43.9% of reference with a coverageData >= 11X There is a 35.97% of reference with a coverageData >= 12X There is a 28.78% of reference with a coverageData >= 13X There is a 22.5% of reference with a coverageData >= 14X There is a 17.22% of reference with a coverageData >= 15X There is a 12.93% of reference with a coverageData >= 16X There is a 9.54% of reference with a coverageData >= 17X There is a 6.94% of reference with a coverageData >= 18X There is a 4.99% of reference with a coverageData >= 19X There is a 3.56% of reference with a coverageData >= 20X There is a 2.53% of reference with a coverageData >= 21X There is a 1.81% of reference with a coverageData >= 22X There is a 1.3% of reference with a coverageData >= 23X There is a 0.96% of reference with a coverageData >= 24X There is a 0.72% of reference with a coverageData >= 25X There is a 0.56% of reference with a coverageData >= 26X There is a 0.45% of reference with a coverageData >= 27X There is a 0.38% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2548716608 10.225517584568024 289.5108780252066 chr2 243199373 2752831906 11.319239322216509 74.72914386395651 chr3 198022430 2129010115 10.751358394097073 7.90645683313503 chr4 191154276 2149882515 11.246845009106675 58.50639460085035 chr5 180915260 1949143833 10.773794499148385 9.141661374777383 chr6 171115067 1856012383 10.846574854802236 41.070584899495664 chr7 159138663 1727115004 10.852893768499236 86.64833328841605 chr8 146364022 1614384092 11.0299243621496 95.33761568541978 chr9 141213431 1366367569 9.67590376725568 187.68479099640592 chr10 135534747 1627709418 12.00953596054597 209.34416821143938 chr11 135006516 1430671589 10.597055841363982 51.6525538943977 chr12 133851895 1400661600 10.464264252665231 9.252765136335935 chr13 115169878 1044391921 9.068273225052822 6.489185730927508 chr14 107349540 960306960 8.945608523334148 8.357387898130249 chr15 102531392 867860281 8.464337253901713 6.320693639757161 chr16 90354753 927974296 10.270342900500209 64.89588820701749 chr17 81195210 838000310 10.320809688157713 74.06210037543782 chr18 78077248 925112298 11.848679630716493 184.14675371870632 chr19 59128983 566881699 9.587205296597102 120.37684667509735 chr20 63025520 632549509 10.036402857128351 23.07975306900451 chr21 48129895 444383508 9.233003894980449 30.809917429171055 chr22 51304566 341799746 6.662170107822372 8.036214485941775 chrMT 16571 15798510 953.3830185263412 129.4710447104953 chrX 155270560 1674156617 10.782189598594865 31.87123083476566 chrY 59373566 80011354 1.3475921927950225 60.7207782083869