BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124963.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,723,048 number of mapped reads = 2,640,831 (96.98%) number of supplementary alignments = 72,221 (2.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,329,718 number of mapped paired reads (second in pair) = 1,311,113 number of mapped paired reads (both in pair) = 2,615,924 number of mapped paired reads (singletons) = 24,907 number of mapped bases = 335,852,047 bp number of sequenced bases = 335,443,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 502,944 duplication rate = 14.83% >>>>>>> Insert size mean insert size = 91,781.5066 std insert size = 2,821,931.2837 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.3565 >>>>>>> ACTG content number of A's = 97,025,547 bp (28.92%) number of C's = 65,919,794 bp (19.65%) number of T's = 99,320,406 bp (29.61%) number of G's = 73,174,895 bp (21.81%) number of N's = 2,491 bp (0%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 4,102,322 number of insertions = 94,571 mapped reads with insertion percentage = 3.26% number of deletions = 174,411 mapped reads with deletion percentage = 6.25% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.1085X std coverageData = 1.9586X There is a 6.09% of reference with a coverageData >= 1X There is a 2.76% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 27913558 0.1119899235877932 0.8848545660300274 chr2 243199373 29280962 0.12039900283788972 2.475862578953947 chr3 198022430 22112587 0.11166708236031646 0.5078843589017324 chr4 191154276 22112851 0.11568065053381281 3.331808478781146 chr5 180915260 18497916 0.10224630028445361 0.4973048202922633 chr6 171115067 17805519 0.10405582227309065 0.5958673953720967 chr7 159138663 19633279 0.12337214998469605 1.0362864170952846 chr8 146364022 18795957 0.1284192436307879 0.5973948285075664 chr9 141213431 13374047 0.09470803807606658 1.5310704375235715 chr10 135534747 19503839 0.14390286942432556 5.932485478459192 chr11 135006516 13822620 0.1023848360030267 0.689920945313397 chr12 133851895 16667021 0.12451837906366585 0.515094173749462 chr13 115169878 8216474 0.07134221328253904 0.3804947977585411 chr14 107349540 9760418 0.09092184279504131 0.5036913783613566 chr15 102531392 9213344 0.08985876247539876 0.4347719531416054 chr16 90354753 12532023 0.13869799411659064 2.6231108944233967 chr17 81195210 8336857 0.1026767096236342 0.9594480488940197 chr18 78077248 7108688 0.09104685656953483 1.4864012220004783 chr19 59128983 5867929 0.0992394711067498 0.6356510970607063 chr20 63025520 7742851 0.12285263175932543 1.2216140647833695 chr21 48129895 4115973 0.08551801328467473 1.5908189036326799 chr22 51304566 3369480 0.0656760257946632 0.43426253050891656 chrMT 16571 177510 10.712087381570212 7.043564373796587 chrX 155270560 11837026 0.07623483807877038 0.47782203624036607 chrY 59373566 8053318 0.13563810534809378 4.618028882957041