BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708531.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 = 2,824,949 number of mapped reads = 1,984,175 (70.24%) number of supplementary alignments = 1,388 (0.05%) number of secondary alignments = 0 number of mapped bases = 94,475,956 bp number of sequenced bases = 94,456,933 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,256 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3539 >>>>>>> ACTG content number of A's = 27,232,327 bp (28.83%) number of C's = 17,563,380 bp (18.59%) number of T's = 30,072,165 bp (31.84%) number of G's = 19,587,819 bp (20.74%) number of N's = 1,242 bp (0%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 489,767 number of insertions = 5,637 mapped reads with insertion percentage = 0.28% number of deletions = 12,475 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.3485X There is a 2.81% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7713585 0.030947104440714714 0.6974712258243696 chr2 243199373 8232849 0.033852262439837785 0.30292984674607243 chr3 198022430 6654949 0.03360704643408325 0.19687151964474559 chr4 191154276 6266755 0.032783755253269875 0.1970145231850116 chr5 180915260 5945715 0.03286464060577311 0.1953866700330998 chr6 171115067 5831151 0.03407736736590238 0.25466951360456297 chr7 159138663 5477413 0.03441912164361969 0.42800471817014524 chr8 146364022 5100854 0.03485046345610809 0.7034635966531972 chr9 141213431 3910822 0.027694405357235462 0.23876268860671584 chr10 135534747 4434728 0.032720229300313666 0.2630357444289365 chr11 135006516 4417103 0.03271770230705013 0.3101679281752776 chr12 133851895 4407984 0.03293180122702036 0.2004373328346054 chr13 115169878 3187393 0.027675578504997633 0.18068524820676493 chr14 107349540 2956042 0.027536606118666183 0.18597830867833215 chr15 102531392 2707086 0.02640250899939016 0.17316276192063773 chr16 90354753 2507222 0.02774864538670146 0.19159695079695213 chr17 81195210 2415572 0.029750178612753142 0.2533829892482343 chr18 78077248 2570745 0.03292566100690434 0.42507782541186534 chr19 59128983 1712902 0.028968906838800188 0.5053688019298277 chr20 63025520 1877356 0.02978723539290116 0.18662042302915552 chr21 48129895 1242823 0.02582226701304875 0.21052834622727679 chr22 51304566 974616 0.018996671758221288 0.1649880819548792 chrMT 16571 143469 8.657835978516685 6.635774067777829 chrX 155270560 3118614 0.020085030929237326 0.17865918457154933 chrY 59373566 668208 0.01125430128283014 0.1291253079935728