BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080749.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 8,214,761 number of mapped reads = 6,042,276 (73.55%) number of supplementary alignments = 30,916 (0.38%) number of secondary alignments = 0 number of mapped bases = 381,022,522 bp number of sequenced bases = 380,889,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 770,112 duplication rate = 9.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1311 >>>>>>> ACTG content number of A's = 120,386,155 bp (31.61%) number of C's = 76,853,582 bp (20.18%) number of T's = 94,536,942 bp (24.82%) number of G's = 88,262,252 bp (23.17%) number of N's = 851,050 bp (0.22%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,911,868 number of insertions = 28,446 mapped reads with insertion percentage = 0.47% number of deletions = 69,105 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.1231X std coverageData = 0.7939X There is a 7.2% of reference with a coverageData >= 1X There is a 2.56% of reference with a coverageData >= 2X There is a 1.11% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 43228306 0.17343309246960711 1.045053608253727 chr2 243199373 26725617 0.10989180058453522 0.7830717132171297 chr3 198022430 22646874 0.11436519590230258 0.5497976327070001 chr4 191154276 23197750 0.12135616573913315 0.7353485437243814 chr5 180915260 28237370 0.15608064239578243 0.6453225330810906 chr6 171115067 25057494 0.14643651455894297 1.3044684040979453 chr7 159138663 25800278 0.16212451150227397 0.9483814862882468 chr8 146364022 16954959 0.11584102956667862 0.8786808013998899 chr9 141213431 13849496 0.09807492036646287 0.5801727274615163 chr10 135534747 16099206 0.11878286827805123 0.9996187041417421 chr11 135006516 15927343 0.11797462427665344 0.6874895921140768 chr12 133851895 13216206 0.09873753374952218 0.5295075068041843 chr13 115169878 13974533 0.12133843712155361 0.5663039305675562 chr14 107349540 11194410 0.10427999970936065 0.6011486649708172 chr15 102531392 10134194 0.09883991431619303 0.5104033944226648 chr16 90354753 12426451 0.13752957744237318 0.7321243004060332 chr17 81195210 9175359 0.11300369812455685 0.577787676145476 chr18 78077248 5954220 0.07626062844837973 0.7761768097780765 chr19 59128983 7972318 0.134829276532627 1.1654663926988558 chr20 63025520 7837079 0.12434770867420054 0.6085797101165794 chr21 48129895 6416600 0.1333183876673739 0.7637785307309748 chr22 51304566 2959841 0.057691570765845676 0.39827222096224335 chrMT 16571 62821 3.791020457425623 4.3055064430357115 chrX 155270560 20677482 0.13317065385737 0.6157617528729862 chrY 59373566 1296315 0.02183320099048792 0.7415497994753575