BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089753.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 30,131,967 number of mapped reads = 25,449,443 (84.46%) number of supplementary alignments = 1,341 (0%) number of secondary alignments = 0 number of mapped bases = 1,203,645,469 bp number of sequenced bases = 1,203,429,580 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,647,778 duplication rate = 13.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1626 >>>>>>> ACTG content number of A's = 360,985,974 bp (30%) number of C's = 242,155,896 bp (20.12%) number of T's = 341,563,447 bp (28.38%) number of G's = 258,550,948 bp (21.48%) number of N's = 173,315 bp (0.01%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 4,788,010 number of insertions = 44,574 mapped reads with insertion percentage = 0.17% number of deletions = 142,795 mapped reads with deletion percentage = 0.56% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 0.3888X std coverageData = 2.5245X There is a 12.92% of reference with a coverageData >= 1X There is a 7.53% of reference with a coverageData >= 2X There is a 4.92% of reference with a coverageData >= 3X There is a 3.4% of reference with a coverageData >= 4X There is a 2.42% of reference with a coverageData >= 5X There is a 1.76% of reference with a coverageData >= 6X There is a 1.29% of reference with a coverageData >= 7X There is a 0.96% of reference with a coverageData >= 8X There is a 0.71% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 96114197 0.38561266814256 4.638995261367642 chr2 243199373 104516658 0.4297571030333207 2.3330543612525076 chr3 198022430 81465454 0.4113950828701577 1.5338019499123348 chr4 191154276 79077626 0.41368483956906094 1.7207797212881581 chr5 180915260 73762760 0.4077199457911953 1.5319325186078665 chr6 171115067 69619822 0.4068596834900576 1.7103983854086025 chr7 159138663 66385113 0.4171526375083345 3.0844106402532847 chr8 146364022 64677500 0.44189479843618945 4.414416076615891 chr9 141213431 50995900 0.361126414384762 2.179124385931161 chr10 135534747 56971068 0.42034289553807186 2.282413362822538 chr11 135006516 54946055 0.406988170852435 2.2920560805664683 chr12 133851895 53228721 0.3976687890746709 1.6087575822931481 chr13 115169878 35858132 0.3113499173803067 1.3317406592944627 chr14 107349540 37582819 0.3500976250107825 1.5048417649508539 chr15 102531392 34267943 0.33421903605873216 1.38123863953082 chr16 90354753 33063459 0.3659293828184113 1.576619794394494 chr17 81195210 29132509 0.35879590680287665 1.7652146737355359 chr18 78077248 31952170 0.4092379126887259 4.320452678993028 chr19 59128983 21012242 0.35536281758811916 3.152635010548746 chr20 63025520 23885927 0.3789881781221321 1.59841428536436 chr21 48129895 15812339 0.328534666447953 1.7164889204725258 chr22 51304566 12915559 0.25174287606292195 1.1879621161228373 chrMT 16571 606472 36.598394786072056 25.811927995088727 chrX 155270560 71866431 0.4628464726346063 1.8890543992759767 chrY 59373566 3928593 0.06616737488868363 1.575283164706811