BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708521.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,588,772 number of mapped reads = 2,553,953 (71.17%) number of supplementary alignments = 585 (0.02%) number of secondary alignments = 0 number of mapped bases = 123,045,792 bp number of sequenced bases = 123,023,325 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,593 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4036 >>>>>>> ACTG content number of A's = 35,754,826 bp (29.06%) number of C's = 23,013,274 bp (18.71%) number of T's = 39,178,329 bp (31.85%) number of G's = 25,075,184 bp (20.38%) number of N's = 1,712 bp (0%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 579,474 number of insertions = 5,883 mapped reads with insertion percentage = 0.23% number of deletions = 14,716 mapped reads with deletion percentage = 0.57% homopolymer indels = 49.18% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3375X There is a 3.47% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 10242177 0.04109188157248363 0.5936406419466529 chr2 243199373 10941304 0.04498903046102837 0.31550291748954823 chr3 198022430 8744718 0.04416023982737713 0.23646568155887998 chr4 191154276 8144138 0.042605052685298024 0.23607055787879594 chr5 180915260 7923330 0.04379580804847529 0.2359776520606641 chr6 171115067 7748981 0.04528520565637858 0.28295965708578763 chr7 159138663 6974128 0.04382422139615437 0.44971093465298656 chr8 146364022 6283994 0.04293400737511845 0.6299479860241871 chr9 141213431 5165338 0.03657823454484298 0.25713256583203126 chr10 135534747 5858648 0.043226169891326834 0.28190166976792547 chr11 135006516 5687570 0.04212811476447552 0.3011764995532564 chr12 133851895 5902042 0.0440938247456265 0.2396407831773068 chr13 115169878 3974577 0.034510560131009255 0.20925534903821086 chr14 107349540 3899195 0.036322419267003844 0.21781126807379594 chr15 102531392 3642315 0.03552390081663965 0.2116638880874653 chr16 90354753 3247038 0.03593654890518045 0.21704723108708832 chr17 81195210 3180610 0.0391723846763867 0.26317185681662847 chr18 78077248 3354644 0.04296570493878063 0.39950567685766813 chr19 59128983 2112782 0.035731749352090156 0.4294797358616462 chr20 63025520 2488743 0.03948786142502275 0.22345533161887654 chr21 48129895 1604965 0.03334653025941569 0.22682629837936627 chr22 51304566 1315872 0.025648243472130725 0.19036272104231025 chrMT 16571 159539 9.627602437994087 7.1034802050402766 chrX 155270560 3750785 0.024156446656726168 0.19388782011861408 chrY 59373566 698359 0.01176211986324015 0.1313163535269878