BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238301.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,192,908 number of mapped reads = 1,048,038 (87.86%) number of supplementary alignments = 11,999 (1.01%) number of secondary alignments = 0 number of mapped bases = 68,573,082 bp number of sequenced bases = 68,537,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,956 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0931 >>>>>>> ACTG content number of A's = 18,736,837 bp (27.34%) number of C's = 12,214,576 bp (17.82%) number of T's = 22,159,264 bp (32.33%) number of G's = 15,369,723 bp (22.43%) number of N's = 56,983 bp (0.08%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 574,152 number of insertions = 5,414 mapped reads with insertion percentage = 0.51% number of deletions = 20,214 mapped reads with deletion percentage = 1.9% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.0222X std coverageData = 0.2489X There is a 1.83% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.05% 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 10140384 0.04068348539841752 0.4702703612455326 chr2 243199373 9098660 0.03741234974318786 0.3186693422375482 chr3 198022430 7345859 0.03709609562916686 0.22562220261850946 chr4 191154276 3012119 0.01575752875127941 0.17819585231591015 chr5 180915260 4132186 0.022840450274896656 0.17699708906569941 chr6 171115067 655468 0.003830568584588755 0.08271986719109715 chr7 159138663 3030848 0.01904532778436124 0.2002917599962311 chr8 146364022 1404529 0.009596135585834066 0.34042111021002425 chr9 141213431 2658274 0.018824512521050493 0.21915138351769722 chr10 135534747 1188769 0.008770953768777833 0.22967484931035723 chr11 135006516 2816502 0.020861970839985235 0.19229267067827147 chr12 133851895 3463047 0.025872229900069776 0.18833075620852038 chr13 115169878 1764597 0.015321688540817939 0.14361352464048624 chr14 107349540 1926839 0.017949205930458574 0.15825871199977762 chr15 102531392 2329307 0.022717988652685022 0.1769873450254389 chr16 90354753 1089837 0.012061756175682312 0.14567742922780255 chr17 81195210 899405 0.011077069694135898 0.12875546738322843 chr18 78077248 2415781 0.030940908675469708 0.3950141417135787 chr19 59128983 1236238 0.020907479501211784 0.29257648255013674 chr20 63025520 2020955 0.03206566165578642 0.21396182932322716 chr21 48129895 1131482 0.02350892309239403 0.19865235731052958 chr22 51304566 1022586 0.01993167625665131 0.1626961050627108 chrMT 16571 2190 0.13215859030837004 0.3946241773368234 chrX 155270560 3553672 0.02288696582275481 0.1871617113944219 chrY 59373566 233548 0.003933535001081121 0.14137810009988008