BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084877.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 = 2,605,057 number of mapped reads = 2,302,546 (88.39%) number of supplementary alignments = 16,552 (0.64%) number of secondary alignments = 0 number of mapped bases = 159,292,473 bp number of sequenced bases = 159,232,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,242 duplication rate = 3.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7369 >>>>>>> ACTG content number of A's = 46,340,824 bp (29.1%) number of C's = 29,040,150 bp (18.24%) number of T's = 51,188,032 bp (32.15%) number of G's = 32,638,470 bp (20.5%) number of N's = 24,921 bp (0.02%) GC percentage = 38.73% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,298,064 number of insertions = 12,651 mapped reads with insertion percentage = 0.55% number of deletions = 33,948 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.72% >>>>>>> Coverage mean coverageData = 0.0515X std coverageData = 0.3879X There is a 4.25% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 12253572 0.04916165083496422 0.6324983816325442 chr2 243199373 13752355 0.05654765812245741 0.4168200774498426 chr3 198022430 13263657 0.0669805789172469 0.30298577886540723 chr4 191154276 9187262 0.04806202713456433 0.25750603769024266 chr5 180915260 8395694 0.04640677629957805 0.2551253577967104 chr6 171115067 9835238 0.057477334827563724 0.286061302510116 chr7 159138663 9324049 0.0585907209739471 0.3696340898765857 chr8 146364022 9359251 0.0639450246864629 0.7208108765673013 chr9 141213431 11446732 0.08105979664214802 0.4463777753242507 chr10 135534747 5117523 0.03775801492439426 0.3043499664824387 chr11 135006516 6736998 0.04990128032042542 0.33452630218342105 chr12 133851895 7371087 0.05506897754417298 0.279381789756285 chr13 115169878 4048262 0.0351503541577078 0.21653493490675677 chr14 107349540 3405601 0.031724411674237264 0.23267921169707584 chr15 102531392 4111022 0.04009525199852939 0.23161765914809887 chr16 90354753 2931563 0.03244503363315043 0.24016449435431922 chr17 81195210 4347192 0.05354000562348444 0.2759923747708954 chr18 78077248 6264536 0.08023510254869638 0.7112829356958935 chr19 59128983 2976287 0.050335501288767306 0.41402689542808596 chr20 63025520 3231417 0.05127156428062791 0.2712184383516747 chr21 48129895 1561187 0.03243695004944432 0.23214823444568825 chr22 51304566 1231366 0.024001099629222086 0.17535639115884125 chrMT 16571 62350 3.7625973085510833 2.6111084258157096 chrX 155270560 8735523 0.056260008336416124 0.2979067077962221 chrY 59373566 342749 0.005772754157969896 0.18014484635791256