BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004014.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 = 2,182,789 number of mapped reads = 1,966,275 (90.08%) number of supplementary alignments = 16,625 (0.76%) number of secondary alignments = 0 number of mapped bases = 131,826,117 bp number of sequenced bases = 131,771,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,603 duplication rate = 4.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9964 >>>>>>> ACTG content number of A's = 37,390,251 bp (28.37%) number of C's = 24,659,954 bp (18.71%) number of T's = 41,475,828 bp (31.48%) number of G's = 28,221,520 bp (21.42%) number of N's = 24,312 bp (0.02%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,122,028 number of insertions = 9,775 mapped reads with insertion percentage = 0.49% number of deletions = 30,911 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.387X There is a 3.18% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% 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% 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 5418135 0.02173769910085801 0.5041191058621977 chr2 243199373 13681052 0.05625447068895198 0.4140595915779341 chr3 198022430 13490346 0.06812534317450807 0.33351131686362817 chr4 191154276 11047511 0.0577936901605068 0.32816104523642076 chr5 180915260 9286828 0.05133247466244694 0.29165548390190904 chr6 171115067 7377663 0.0431152155642729 0.28232361385304006 chr7 159138663 9472303 0.059522323622889804 0.6667591086307385 chr8 146364022 8913847 0.06090189978518081 0.7071149597933255 chr9 141213431 4951673 0.03506517025282106 0.32297385583954186 chr10 135534747 4568106 0.03370431642890808 0.3465257673461475 chr11 135006516 4814803 0.03566348604981407 0.28884383867757335 chr12 133851895 6382597 0.04768402419704256 0.2844183940190031 chr13 115169878 5581803 0.04846582367656932 0.2847233732225012 chr14 107349540 2533321 0.02359880629204373 0.2201540764885366 chr15 102531392 3254804 0.031744463198158865 0.22584597762272002 chr16 90354753 2215505 0.024520071456561893 0.2303203723914334 chr17 81195210 4595947 0.056603671571266334 0.32117637668588694 chr18 78077248 2279538 0.029195931700871425 0.606107841978009 chr19 59128983 2240290 0.03788818759152343 0.3824719821118885 chr20 63025520 2917943 0.04629780127161188 0.2980666813801721 chr21 48129895 2622786 0.05449390654186966 0.31992090660133715 chr22 51304566 831767 0.01621233868346143 0.156221395670431 chrMT 16571 53245 3.2131434433649146 3.0907206662692244 chrX 155270560 3026870 0.0194941655391724 0.19270090381232582 chrY 59373566 267434 0.004504260363947148 0.13531672208849446