BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068963.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 = 2,840,331 number of mapped reads = 2,359,291 (83.06%) number of supplementary alignments = 13,999 (0.49%) number of secondary alignments = 0 number of mapped bases = 155,142,180 bp number of sequenced bases = 155,078,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,413 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9805 >>>>>>> ACTG content number of A's = 42,208,268 bp (27.22%) number of C's = 26,925,562 bp (17.36%) number of T's = 51,316,723 bp (33.09%) number of G's = 34,248,775 bp (22.08%) number of N's = 378,853 bp (0.24%) GC percentage = 39.45% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,499,791 number of insertions = 13,327 mapped reads with insertion percentage = 0.56% number of deletions = 39,150 mapped reads with deletion percentage = 1.64% homopolymer indels = 49.16% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 0.4523X There is a 4.18% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 20902815 0.08386263960401527 1.0260413700416051 chr2 243199373 19742662 0.08117891817097736 0.47142675222813696 chr3 198022430 10629717 0.05367935844439441 0.2744473676567279 chr4 191154276 3415320 0.017866825014157674 0.16788751331287383 chr5 180915260 7680668 0.042454506048854035 0.24299208377277903 chr6 171115067 11010558 0.06434592928044144 0.3427562728692862 chr7 159138663 9180157 0.05768652838311203 0.5382818368705632 chr8 146364022 10698116 0.07309252542950753 0.5080723618871553 chr9 141213431 5697732 0.040348371678611786 0.33781896638534603 chr10 135534747 9214592 0.0679869347452281 0.529512356805083 chr11 135006516 7993692 0.059209675479663514 0.41393582536519924 chr12 133851895 3199450 0.023902911497816298 0.18261193272387716 chr13 115169878 4894517 0.04249823899266438 0.23601732537041736 chr14 107349540 5994172 0.05583789180652288 0.28864148162699416 chr15 102531392 3092207 0.030158636683680254 0.19860488522085556 chr16 90354753 1850860 0.02048436787824543 0.1991068274579976 chr17 81195210 2220073 0.027342413425619567 0.2121950771467215 chr18 78077248 4475034 0.057315467881244996 0.6562194627083676 chr19 59128983 3394740 0.057412453720031 0.585594283393299 chr20 63025520 1256737 0.019940129014405592 0.18266705166304287 chr21 48129895 1911784 0.03972134159029435 0.24546604977201655 chr22 51304566 869358 0.016945041499815044 0.14709571695920362 chrMT 16571 157682 9.51553919497918 6.334945017488002 chrX 155270560 5390924 0.03471955018388547 0.24399370931236053 chrY 59373566 268613 0.004524117685638084 0.10322257370288328