BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708508.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 = 3,439,097 number of mapped reads = 2,341,245 (68.08%) number of supplementary alignments = 562 (0.02%) number of secondary alignments = 0 number of mapped bases = 111,311,568 bp number of sequenced bases = 111,284,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,559 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2858 >>>>>>> ACTG content number of A's = 31,630,611 bp (28.42%) number of C's = 20,580,374 bp (18.49%) number of T's = 35,658,020 bp (32.04%) number of G's = 23,414,204 bp (21.04%) number of N's = 1,508 bp (0%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 544,977 number of insertions = 5,956 mapped reads with insertion percentage = 0.25% number of deletions = 17,616 mapped reads with deletion percentage = 0.75% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.3335X There is a 3.07% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 9344378 0.037489888540739084 0.4561155849896736 chr2 243199373 9839246 0.040457530291412386 0.5595259093677379 chr3 198022430 7955816 0.040176337599735545 0.24031501542738543 chr4 191154276 7199441 0.03766298693731549 0.2388024475155041 chr5 180915260 6899938 0.03813906024290046 0.2299886134059344 chr6 171115067 6689644 0.03909441826066667 0.31393274881642264 chr7 159138663 6184019 0.038859312271587954 0.3725681982239972 chr8 146364022 5775971 0.039463051924058225 0.5985533167951532 chr9 141213431 4682854 0.03316153404699869 0.25878288817350636 chr10 135534747 5242819 0.03868247158789473 0.2554861321350757 chr11 135006516 5092680 0.03772173485315331 0.26862207061210164 chr12 133851895 5260474 0.03930070620217965 0.2356846441486882 chr13 115169878 3461776 0.030057998324874494 0.23953400723658852 chr14 107349540 3572270 0.03327699401413364 0.2175096018118013 chr15 102531392 3363429 0.03280389483057052 0.21957556571372314 chr16 90354753 3019934 0.033423078473802034 0.2179812499104514 chr17 81195210 3126677 0.03850814598545899 0.2439311200467668 chr18 78077248 2863649 0.036677125197855334 0.32884583273303036 chr19 59128983 2118308 0.03582520605842316 0.3367383546220229 chr20 63025520 2366253 0.03754436298185243 0.23034986740844382 chr21 48129895 1471080 0.03056478722839516 0.2198985254326852 chr22 51304566 1280602 0.024960780293902106 0.18816110162273664 chrMT 16571 138204 8.34011224428218 5.569296130874154 chrX 155270560 3642279 0.02345762776923069 0.20122397330508743 chrY 59373566 719827 0.01212369491163795 0.14109422085869505