BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124910.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 = 5,075,232 number of mapped reads = 5,013,313 (98.78%) number of supplementary alignments = 49,422 (0.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,522,249 number of mapped paired reads (second in pair) = 2,491,064 number of mapped paired reads (both in pair) = 4,979,142 number of mapped paired reads (singletons) = 34,171 number of mapped bases = 672,627,151 bp number of sequenced bases = 672,205,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 955,444 duplication rate = 13.65% >>>>>>> Insert size mean insert size = 40,145.0512 std insert size = 1,905,813.0647 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 53.6918 >>>>>>> ACTG content number of A's = 194,375,193 bp (28.92%) number of C's = 131,229,862 bp (19.52%) number of T's = 197,895,613 bp (29.44%) number of G's = 148,704,253 bp (22.12%) number of N's = 303 bp (0%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 5,533,128 number of insertions = 100,899 mapped reads with insertion percentage = 1.9% number of deletions = 204,937 mapped reads with deletion percentage = 3.94% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.2173X std coverageData = 4.1791X There is a 10.78% of reference with a coverageData >= 1X There is a 5.17% of reference with a coverageData >= 2X There is a 2.04% of reference with a coverageData >= 3X There is a 1.1% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 49202092 0.19740007789188216 1.2812118864759838 chr2 243199373 55247627 0.22717010458739959 2.170325212029026 chr3 198022430 43180024 0.21805622726677984 0.8721831485165655 chr4 191154276 38558632 0.20171472387047204 1.5766783039174792 chr5 180915260 38432755 0.21243512017725869 0.7690159740474062 chr6 171115067 34176557 0.19972850783502308 0.9053665923205112 chr7 159138663 47280718 0.2971039036566494 2.1860671211767073 chr8 146364022 25477881 0.174072020240056 0.7388678788617008 chr9 141213431 27922936 0.19773569555150883 2.076318255685197 chr10 135534747 43756115 0.32284057017496776 16.654319815988845 chr11 135006516 31321216 0.2319978096464618 2.630423307250366 chr12 133851895 39955276 0.2985036259665954 0.9453126733599974 chr13 115169878 15810137 0.13727666708130054 0.5882779896360973 chr14 107349540 15342267 0.1429187959259071 0.6320486040264318 chr15 102531392 24056651 0.23462717642612324 0.8149303168496257 chr16 90354753 29396891 0.32534969134385217 10.572310431990214 chr17 81195210 14862298 0.18304402439503512 1.1601453190831383 chr18 78077248 12244851 0.15682995128106975 2.037586346124468 chr19 59128983 5426547 0.0917747393017059 0.9191685687787722 chr20 63025520 17881045 0.28371118556419683 0.9978432021365602 chr21 48129895 5404941 0.11229903992103037 0.9311704121359757 chr22 51304566 4273374 0.08329422375388576 0.6122717057219065 chrMT 16571 316288 19.086838452718606 12.041925822669489 chrX 155270560 45788543 0.2948952009962481 1.3542741843754056 chrY 59373566 7311489 0.1231438414866306 2.5354069988555152