BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068937.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 = 1,285,766 number of mapped reads = 854,149 (66.43%) number of supplementary alignments = 5,083 (0.4%) number of secondary alignments = 0 number of mapped bases = 55,211,005 bp number of sequenced bases = 55,183,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,043 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3668 >>>>>>> ACTG content number of A's = 14,940,879 bp (27.08%) number of C's = 9,371,722 bp (16.98%) number of T's = 18,485,093 bp (33.5%) number of G's = 12,260,385 bp (22.22%) number of N's = 125,136 bp (0.23%) GC percentage = 39.2% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 565,079 number of insertions = 4,719 mapped reads with insertion percentage = 0.55% number of deletions = 17,287 mapped reads with deletion percentage = 2% homopolymer indels = 48.82% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.19X There is a 1.34% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.09% 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 3478000 0.013953826819151636 0.19954843303288403 chr2 243199373 3062092 0.012590871276629483 0.16378856024599348 chr3 198022430 2218824 0.011204912494003835 0.1355683245968637 chr4 191154276 2264799 0.011848016415808559 0.1413546612712558 chr5 180915260 2023419 0.011184346748859106 0.13628498428992292 chr6 171115067 10226739 0.05976527479020886 0.3657931217997191 chr7 159138663 1882418 0.011828791096479175 0.15770149369008823 chr8 146364022 5885026 0.04020814623418862 0.27294498416177837 chr9 141213431 1431059 0.010134014802033952 0.1381409367519835 chr10 135534747 5945556 0.04386739291290373 0.2995336275984258 chr11 135006516 2428476 0.017987842897893905 0.19218940482917815 chr12 133851895 1685366 0.012591274856437408 0.14475676402073756 chr13 115169878 818703 0.007108655615663672 0.10718213794891632 chr14 107349540 812775 0.0075712946697303034 0.11327528503569832 chr15 102531392 729376 0.0071136847532509845 0.1070472492495748 chr16 90354753 774257 0.0085690788175803 0.1191996078851409 chr17 81195210 754668 0.009294489169989215 0.12587719762612892 chr18 78077248 2381335 0.030499730215901053 0.25380761034500404 chr19 59128983 483987 0.008185275231268564 0.1477349159693379 chr20 63025520 570873 0.009057807059743418 0.12228148969651795 chr21 48129895 426859 0.008868895309245948 0.11990313785073596 chr22 51304566 325615 0.006346706061211004 0.09905378136223067 chrMT 16571 91872 5.544143383018526 3.843356312223931 chrX 155270560 4411977 0.028414768388804676 0.2222375485946544 chrY 59373566 96934 0.0016326120617380468 0.05004953300707713