BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238619.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 = 2,938,017 number of mapped reads = 2,523,812 (85.9%) number of supplementary alignments = 22,981 (0.78%) number of secondary alignments = 0 number of mapped bases = 153,359,568 bp number of sequenced bases = 153,272,553 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,087,707 duplication rate = 22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.8498 >>>>>>> ACTG content number of A's = 37,917,074 bp (24.74%) number of C's = 25,796,066 bp (16.83%) number of T's = 53,479,770 bp (34.89%) number of G's = 36,076,303 bp (23.54%) number of N's = 3,340 bp (0%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,018,880 number of insertions = 9,869 mapped reads with insertion percentage = 0.39% number of deletions = 53,036 mapped reads with deletion percentage = 2.08% homopolymer indels = 40.25% >>>>>>> Coverage mean coverageData = 0.0495X std coverageData = 1.1613X There is a 1.32% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 14927175 0.05988821588532772 1.258587908485425 chr2 243199373 5125354 0.021074700714791728 2.640118056158549 chr3 198022430 4585822 0.023158093757358698 0.44986600608874894 chr4 191154276 21263952 0.11123974019812144 1.0185588326719242 chr5 180915260 12092480 0.06684057497416193 0.7838516899566956 chr6 171115067 2595525 0.015168301923991299 0.8535583052524599 chr7 159138663 17193441 0.10804062743696671 1.4054659242565304 chr8 146364022 6888208 0.047062166684651505 1.012108881647294 chr9 141213431 1897421 0.01343654768929168 0.49656464557544483 chr10 135534747 3180310 0.023464905276283136 0.6489276257491466 chr11 135006516 12365056 0.09158858673162117 0.9435529196767981 chr12 133851895 14479646 0.10817662312513394 0.9882857143157003 chr13 115169878 1899414 0.016492281080648534 0.6842300673139592 chr14 107349540 1521285 0.014171322951174266 0.3398278133246906 chr15 102531392 5126075 0.049995176111526894 0.8338581138232988 chr16 90354753 2520672 0.027897503078781034 0.5154396267905134 chr17 81195210 1115792 0.013742091436182012 0.2980616057673237 chr18 78077248 8105746 0.1038170044108112 2.4319540278643568 chr19 59128983 2461376 0.04162723380512058 0.8552891630312026 chr20 63025520 4304476 0.0682973500258308 0.7969614167620807 chr21 48129895 1221834 0.025386176304768585 0.4557606907895689 chr22 51304566 421805 0.008221587918704936 0.2218633750108285 chrMT 16571 20826 1.2567738820831573 2.818996550216697 chrX 155270560 7622444 0.04909136670853766 0.6531408868737202 chrY 59373566 423433 0.007131675399116166 0.33643418924523644