BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124983.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 = 4,689,630 number of mapped reads = 4,542,630 (96.87%) number of supplementary alignments = 10,893 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,301,435 number of mapped paired reads (second in pair) = 2,241,195 number of mapped paired reads (both in pair) = 4,466,320 number of mapped paired reads (singletons) = 76,310 number of mapped bases = 278,362,765 bp number of sequenced bases = 278,254,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,680 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 68,806.9561 std insert size = 2,552,095.6658 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 51.7883 >>>>>>> ACTG content number of A's = 76,642,657 bp (27.54%) number of C's = 49,699,174 bp (17.86%) number of T's = 82,679,075 bp (29.71%) number of G's = 69,234,064 bp (24.88%) number of N's = 2 bp (0%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,722,732 number of insertions = 29,280 mapped reads with insertion percentage = 0.64% number of deletions = 66,760 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0899X std coverageData = 0.6722X There is a 7.14% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% 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 23074357 0.09257492281232872 0.5017391479977475 chr2 243199373 25058948 0.10303870314665654 0.8758553585631336 chr3 198022430 19728672 0.09962847138074207 0.3829961730630304 chr4 191154276 16744879 0.08759876760486383 0.5364881362975904 chr5 180915260 16789804 0.0928047971188279 0.38231352656088025 chr6 171115067 17520441 0.10238982052936343 0.44393264707896946 chr7 159138663 15155005 0.09523144605029138 0.4816998633983112 chr8 146364022 15905189 0.10866870684928295 0.4239736472677146 chr9 141213431 12524366 0.08869103959381881 0.5323446257437109 chr10 135534747 14642128 0.10803228193579023 1.9871461360842004 chr11 135006516 12148479 0.08998439008677181 0.40412146468388316 chr12 133851895 12656430 0.09455547865048904 0.3684523292340147 chr13 115169878 7818444 0.06788618808817354 0.3050021189952258 chr14 107349540 7717015 0.07188680081908129 0.3508388025173847 chr15 102531392 7704760 0.07514537596446559 0.3356468875566266 chr16 90354753 9529354 0.10546599579548405 1.1548498500517728 chr17 81195210 6729849 0.08288480317989201 0.5158591008948425 chr18 78077248 6961465 0.08916124963830692 0.6642457205329309 chr19 59128983 4596220 0.07773209967098538 0.4837965036720633 chr20 63025520 6058534 0.0961282667719362 0.45666044807186884 chr21 48129895 3484310 0.07239388326112077 0.40525012102460367 chr22 51304566 3035555 0.059167345845981816 0.3271052916150837 chrMT 16571 44722 2.6988111761511075 2.525612624556305 chrX 155270560 9803638 0.06313906512606124 0.354791007558182 chrY 59373566 2930201 0.04935194561162117 0.9523514640543006