BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240040.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,253,891 number of mapped reads = 1,795,259 (79.65%) number of supplementary alignments = 14,928 (0.66%) number of secondary alignments = 0 number of mapped bases = 113,916,753 bp number of sequenced bases = 113,873,580 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 317,765 duplication rate = 12.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8467 >>>>>>> ACTG content number of A's = 31,601,002 bp (27.75%) number of C's = 20,309,261 bp (17.83%) number of T's = 36,708,640 bp (32.24%) number of G's = 25,173,988 bp (22.11%) number of N's = 80,689 bp (0.07%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 971,072 number of insertions = 7,879 mapped reads with insertion percentage = 0.44% number of deletions = 25,567 mapped reads with deletion percentage = 1.41% homopolymer indels = 47.49% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.4426X There is a 1.69% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 8546121 0.03428726061228148 0.6200824522748085 chr2 243199373 10216089 0.04200705320074982 0.5281521663829618 chr3 198022430 7780515 0.03929107929844109 0.3788473450869723 chr4 191154276 7946539 0.041571337907188644 0.43281482628578766 chr5 180915260 6900301 0.03814106670714234 0.37285066773929043 chr6 171115067 7088963 0.041428046777435446 0.42858670872233473 chr7 159138663 6480943 0.0407251316419568 0.5051155812251916 chr8 146364022 6543601 0.04470771512414438 0.49290241594140316 chr9 141213431 5130376 0.036330651862711276 0.4272253775481365 chr10 135534747 4903110 0.03617603683577909 0.45020177728790006 chr11 135006516 5012236 0.03712588213149653 0.37866505858032806 chr12 133851895 4865278 0.0363482190521098 0.3660778339260567 chr13 115169878 3493598 0.030334303210775303 0.33753874758932134 chr14 107349540 3451138 0.032148605387596445 0.3804987526798765 chr15 102531392 2994582 0.029206489267209014 0.4039138662548019 chr16 90354753 2913848 0.03224897311157499 0.3412092561229985 chr17 81195210 2647507 0.03260668948328356 0.3496789407998653 chr18 78077248 3242073 0.041523914879786746 0.6354131250072639 chr19 59128983 1645621 0.027831038460445025 0.4546721270773091 chr20 63025520 2250367 0.035705647490096075 0.35399708908250016 chr21 48129895 1489482 0.03094712755970068 0.32795039687919986 chr22 51304566 965394 0.018816921675158502 0.24063903931307393 chrMT 16571 31638 1.909239032043932 3.2943756590151696 chrX 155270560 7104078 0.04575289739407135 0.42586563881734124 chrY 59373566 273355 0.004603984877714773 0.13091601201559042