BamQC report ----------------------------------- >>>>>>> Input bam file = SRR631031.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 111,523,710 number of mapped reads = 111,266,249 (99.77%) number of supplementary alignments = 662,227 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 55,717,912 number of mapped paired reads (second in pair) = 55,548,337 number of mapped paired reads (both in pair) = 111,073,164 number of mapped paired reads (singletons) = 193,085 number of mapped bases = 11,113,763,774 bp number of sequenced bases = 11,111,471,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,275,992 duplication rate = 20.55% >>>>>>> Insert size mean insert size = 33,362.2379 std insert size = 1,713,691.5945 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 53.923 >>>>>>> ACTG content number of A's = 3,463,442,044 bp (31.17%) number of C's = 2,086,817,657 bp (18.78%) number of T's = 3,450,280,312 bp (31.05%) number of G's = 2,109,991,726 bp (18.99%) number of N's = 939,459 bp (0.01%) GC percentage = 37.77% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 76,497,932 number of insertions = 937,959 mapped reads with insertion percentage = 0.83% number of deletions = 1,015,892 mapped reads with deletion percentage = 0.89% homopolymer indels = 44.94% >>>>>>> Coverage mean coverageData = 3.5901X std coverageData = 16.1863X There is a 30.22% of reference with a coverageData >= 1X There is a 21.72% of reference with a coverageData >= 2X There is a 17.53% of reference with a coverageData >= 3X There is a 14.87% of reference with a coverageData >= 4X There is a 12.96% of reference with a coverageData >= 5X There is a 11.52% of reference with a coverageData >= 6X There is a 10.37% of reference with a coverageData >= 7X There is a 9.43% of reference with a coverageData >= 8X There is a 8.64% of reference with a coverageData >= 9X There is a 7.97% of reference with a coverageData >= 10X There is a 7.39% of reference with a coverageData >= 11X There is a 6.88% of reference with a coverageData >= 12X There is a 6.44% of reference with a coverageData >= 13X There is a 6.04% of reference with a coverageData >= 14X There is a 5.69% of reference with a coverageData >= 15X There is a 5.37% of reference with a coverageData >= 16X There is a 5.08% of reference with a coverageData >= 17X There is a 4.81% of reference with a coverageData >= 18X There is a 4.57% of reference with a coverageData >= 19X There is a 4.35% of reference with a coverageData >= 20X There is a 4.15% of reference with a coverageData >= 21X There is a 3.96% of reference with a coverageData >= 22X There is a 3.78% of reference with a coverageData >= 23X There is a 3.62% of reference with a coverageData >= 24X There is a 3.47% of reference with a coverageData >= 25X There is a 3.33% of reference with a coverageData >= 26X There is a 3.2% of reference with a coverageData >= 27X There is a 3.08% of reference with a coverageData >= 28X There is a 2.96% of reference with a coverageData >= 29X There is a 2.85% of reference with a coverageData >= 30X There is a 2.75% of reference with a coverageData >= 31X There is a 2.65% of reference with a coverageData >= 32X There is a 2.56% of reference with a coverageData >= 33X There is a 2.48% of reference with a coverageData >= 34X There is a 2.39% of reference with a coverageData >= 35X There is a 2.32% of reference with a coverageData >= 36X There is a 2.24% of reference with a coverageData >= 37X There is a 2.17% of reference with a coverageData >= 38X There is a 2.11% of reference with a coverageData >= 39X There is a 2.04% of reference with a coverageData >= 40X There is a 1.98% of reference with a coverageData >= 41X There is a 1.92% of reference with a coverageData >= 42X There is a 1.87% of reference with a coverageData >= 43X There is a 1.82% of reference with a coverageData >= 44X There is a 1.76% of reference with a coverageData >= 45X There is a 1.72% of reference with a coverageData >= 46X There is a 1.67% of reference with a coverageData >= 47X There is a 1.62% of reference with a coverageData >= 48X There is a 1.58% of reference with a coverageData >= 49X There is a 1.54% of reference with a coverageData >= 50X There is a 1.5% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 867257455 3.4794595556895325 15.391771532853683 chr2 243199373 926771249 3.810746868167296 16.323086932437388 chr3 198022430 878901996 4.438396175625155 16.569337910482883 chr4 191154276 902095422 4.719200851149153 19.892239885277192 chr5 180915260 784960146 4.33882772520129 16.861693997978957 chr6 171115067 751168845 4.389846307338909 17.421040961436262 chr7 159138663 609472255 3.8298188731169622 17.893578727449636 chr8 146364022 538043847 3.6760662876564023 14.8451967530379 chr9 141213431 478315934 3.3871844244050697 19.56084851193651 chr10 135534747 378569194 2.7931523272035914 11.187283299139601 chr11 135006516 540527659 4.00371533919148 15.797906518559675 chr12 133851895 459822973 3.43531164052627 15.084732766117005 chr13 115169878 488808707 4.244240902990277 19.943828259076053 chr14 107349540 299681154 2.7916389208561116 13.751165458570892 chr15 102531392 220275706 2.148373309902981 10.033337978716938 chr16 90354753 246227563 2.7251202047998517 14.92400637779569 chr17 81195210 172179231 2.120558971397451 10.680017115223237 chr18 78077248 271395629 3.475988664457026 17.229238302103166 chr19 59128983 67716631 1.145235848213388 5.613961375811201 chr20 63025520 174243576 2.7646511444887722 12.453671654986156 chr21 48129895 136610617 2.838373468298653 11.739031897893176 chr22 51304566 63827883 1.2440975136598953 8.23125238677842 chrMT 16571 481 0.02902661275722648 0.24032020048408942 chrX 155270560 849642370 5.4720120156712255 22.867988463426553 chrY 59373566 7247251 0.12206191219843525 2.097990670342105