BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472817.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,696,196 number of mapped reads = 2,168,976 (80.45%) number of supplementary alignments = 10,575 (0.39%) number of secondary alignments = 0 number of mapped bases = 138,390,996 bp number of sequenced bases = 138,331,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,063 duplication rate = 4.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4681 >>>>>>> ACTG content number of A's = 36,383,107 bp (26.3%) number of C's = 26,711,257 bp (19.31%) number of T's = 42,443,698 bp (30.68%) number of G's = 32,790,729 bp (23.7%) number of N's = 2,573 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,201,877 number of insertions = 10,060 mapped reads with insertion percentage = 0.46% number of deletions = 33,702 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0447X std coverageData = 0.3488X There is a 3.55% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11729291 0.047058221772695204 0.43599200381579134 chr2 243199373 14194241 0.058364628267359886 0.4800120558734257 chr3 198022430 8446517 0.04265434476286348 0.2513980889438517 chr4 191154276 6701213 0.035056568653478615 0.24536584644965834 chr5 180915260 7760944 0.04289822760114321 0.25343202242123186 chr6 171115067 8747182 0.05111871300029938 0.31253007632370916 chr7 159138663 7779694 0.048886259651433665 0.4687724894871416 chr8 146364022 8122261 0.05549356248217885 0.37394927143491363 chr9 141213431 5603543 0.039681374217159275 0.35878779723312604 chr10 135534747 6632219 0.048933717344084464 0.3431565860719514 chr11 135006516 5456040 0.04041316050256419 0.37815269099318755 chr12 133851895 5569757 0.041611342147976314 0.2540156556169064 chr13 115169878 5706393 0.04954761695588494 0.2789707347058744 chr14 107349540 3663296 0.03412493430339804 0.24651920921454837 chr15 102531392 3524822 0.034377978599958926 0.2385883529195658 chr16 90354753 4315124 0.04775757618417705 0.28535812007828737 chr17 81195210 3561924 0.04386864693126602 0.2813746922923353 chr18 78077248 2762723 0.03538448230142538 0.6119385940407464 chr19 59128983 3025972 0.05117578294894739 0.3679505981729535 chr20 63025520 4513816 0.07161886169285077 0.3416489985397238 chr21 48129895 2273959 0.04724629048120716 0.29364374305737645 chr22 51304566 1509664 0.029425529103978776 0.21823449647822737 chrMT 16571 223780 13.50431476676121 8.869857441614819 chrX 155270560 5901608 0.038008544568912485 0.2660898885984594 chrY 59373566 665013 0.011200489456873788 0.15915843173305347