BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819050.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 950,240 number of mapped reads = 852,315 (89.69%) number of supplementary alignments = 3,720 (0.39%) number of secondary alignments = 0 number of mapped bases = 48,208,346 bp number of sequenced bases = 48,195,089 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,671 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5191 >>>>>>> ACTG content number of A's = 11,670,890 bp (24.22%) number of C's = 10,017,533 bp (20.79%) number of T's = 15,177,704 bp (31.49%) number of G's = 11,327,964 bp (23.5%) number of N's = 998 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 236,952 number of insertions = 3,460 mapped reads with insertion percentage = 0.4% number of deletions = 7,873 mapped reads with deletion percentage = 0.92% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 0.1504X There is a 1.46% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5395993 0.02164886481867582 0.21263114202494773 chr2 243199373 4001848 0.016455009528334598 0.1661908338352495 chr3 198022430 3130574 0.01580918888834967 0.1332290134030398 chr4 191154276 3030021 0.01585118085456796 0.1395445530559809 chr5 180915260 2370436 0.013102465762147427 0.1206011643785428 chr6 171115067 2534568 0.014812067951912148 0.13260013146939967 chr7 159138663 2085819 0.013106928012836201 0.13415173618172785 chr8 146364022 3011218 0.020573484923774504 0.16053320916855077 chr9 141213431 1778561 0.012594843050021213 0.14740801690080685 chr10 135534747 2305617 0.017011261326219173 0.16582119483192503 chr11 135006516 1539861 0.01140582725651553 0.12880355156125153 chr12 133851895 2175910 0.016256101566585964 0.13432126641796063 chr13 115169878 1472730 0.012787458192844487 0.11837261528495514 chr14 107349540 1664228 0.0155028889737208 0.13450157596682083 chr15 102531392 1376273 0.01342294270227015 0.12096631794247976 chr16 90354753 1450038 0.016048275844437316 0.139454614436127 chr17 81195210 1116086 0.013745712339434802 0.12588281751169442 chr18 78077248 1166549 0.014940959496933089 0.23578841894079816 chr19 59128983 965553 0.016329606074909152 0.16598382374605816 chr20 63025520 1624912 0.02578181028891154 0.1723391679334797 chr21 48129895 617405 0.012827890025523637 0.12539626412631663 chr22 51304566 585876 0.011419568386954097 0.11218487754949819 chrMT 16571 6408 0.38669965602558687 0.6729143145016936 chrX 155270560 2659508 0.01712821799573596 0.14824875622456152 chrY 59373566 142354 0.0023975989584321075 0.06557165640454958