BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081694.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 = 1,742,175 number of mapped reads = 1,494,665 (85.79%) number of supplementary alignments = 15,005 (0.86%) number of secondary alignments = 0 number of mapped bases = 99,781,612 bp number of sequenced bases = 99,745,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,391 duplication rate = 4.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6368 >>>>>>> ACTG content number of A's = 28,219,839 bp (28.29%) number of C's = 17,266,435 bp (17.31%) number of T's = 32,981,805 bp (33.07%) number of G's = 21,209,612 bp (21.26%) number of N's = 67,861 bp (0.07%) GC percentage = 38.57% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 848,376 number of insertions = 8,131 mapped reads with insertion percentage = 0.54% number of deletions = 22,426 mapped reads with deletion percentage = 1.49% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.2572X There is a 2.58% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 7313159 0.02934058487260499 0.29760460534360533 chr2 243199373 7967192 0.032759919985484505 0.26382049906531735 chr3 198022430 7832243 0.039552302231620935 0.23994263556819423 chr4 191154276 7288174 0.03812718267416629 0.23959172188963235 chr5 180915260 6016755 0.0332573106326133 0.22102347639922182 chr6 171115067 6128168 0.03581314087321136 0.2453004239458737 chr7 159138663 6153432 0.03866710882194605 0.30424050948216724 chr8 146364022 5118596 0.03497168177026455 0.4596145300023884 chr9 141213431 3366837 0.023842186795957107 0.21892505043187488 chr10 135534747 5246903 0.03871260408225796 0.26043056488538197 chr11 135006516 4612499 0.03416501022809892 0.2365290225724455 chr12 133851895 4601506 0.0343775932346718 0.22494587185909465 chr13 115169878 3735331 0.03243322876490327 0.2174047817726372 chr14 107349540 3332290 0.031041493051577117 0.2164441592715085 chr15 102531392 2451879 0.0239134469177986 0.1868987946222186 chr16 90354753 2484926 0.027501884709927767 0.20317989245370088 chr17 81195210 2044029 0.02517425596904054 0.19518319688564548 chr18 78077248 2356470 0.030181263560928786 0.31705179148364265 chr19 59128983 1390398 0.023514661160331473 0.24598355367119817 chr20 63025520 1804565 0.028632290538816656 0.2057876338749919 chr21 48129895 1309125 0.02719983079123692 0.20241245123956172 chr22 51304566 744363 0.014508708640084782 0.14299818002237588 chrMT 16571 22434 1.353810874419166 1.510465823722272 chrX 155270560 6238190 0.04017625749530368 0.2495012655143827 chrY 59373566 222148 0.0037415303638659667 0.08474160225653007