BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975282.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,208,050 number of mapped reads = 5,156,541 (99.01%) number of supplementary alignments = 30,518 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,577,358 number of mapped paired reads (second in pair) = 2,579,183 number of mapped paired reads (both in pair) = 5,131,730 number of mapped paired reads (singletons) = 24,811 number of mapped bases = 486,100,360 bp number of sequenced bases = 485,816,354 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 467,463 duplication rate = 3.92% >>>>>>> Insert size mean insert size = 65,695.9809 std insert size = 2,359,220.243 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.6064 >>>>>>> ACTG content number of A's = 143,763,151 bp (29.59%) number of C's = 96,233,338 bp (19.81%) number of T's = 146,621,711 bp (30.18%) number of G's = 99,185,400 bp (20.42%) number of N's = 12,754 bp (0%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 4,009,903 number of insertions = 76,566 mapped reads with insertion percentage = 1.45% number of deletions = 143,396 mapped reads with deletion percentage = 2.72% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.157X std coverageData = 2.6185X There is a 10.22% of reference with a coverageData >= 1X There is a 2.96% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 39423311 0.15816735317181016 2.39145974886396 chr2 243199373 43305797 0.17806705858571437 2.677184792239125 chr3 198022430 33773666 0.17055474978263827 0.6725466515875237 chr4 191154276 33846489 0.17706372940357348 2.469582185269009 chr5 180915260 29632701 0.16379326431612237 0.532492252567263 chr6 171115067 34436600 0.20124820451959383 1.5339569649011655 chr7 159138663 25866366 0.16253979713276842 1.9553527596182387 chr8 146364022 24798917 0.16943314799042622 0.945125323656308 chr9 141213431 20779271 0.14714797914654448 3.5582608057692826 chr10 135534747 28557996 0.21070608557671192 7.829523381738639 chr11 135006516 18784945 0.1391410248672738 1.859976140609693 chr12 133851895 20634897 0.1541621581076607 0.5198994793106426 chr13 115169878 15235081 0.1322835559485441 0.46858276027295986 chr14 107349540 13670164 0.127342548463645 0.5543477334460044 chr15 102531392 12396845 0.12090779963272126 0.4515205721923131 chr16 90354753 17012263 0.18828298938518487 4.1927241638453365 chr17 81195210 8628220 0.10626513559112662 1.486057940657457 chr18 78077248 13723053 0.1757625089449874 3.5036199645143045 chr19 59128983 4999112 0.08454588167024621 1.3723269715369368 chr20 63025520 8614909 0.13668921732022202 0.7062802731400798 chr21 48129895 5883792 0.12224817860084673 1.0128747425518456 chr22 51304566 3589178 0.06995825673683703 0.3582374487512385 chrMT 16571 64898 3.9163599058596343 6.0068449272155515 chrX 155270560 15942746 0.10267719778945861 0.8653927563405385 chrY 59373566 12499143 0.21051696642239748 5.634366606159907