BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234040.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 = 4,125,681 number of mapped reads = 147,235 (3.57%) number of supplementary alignments = 1,165 (0.03%) number of secondary alignments = 0 number of mapped bases = 9,425,347 bp number of sequenced bases = 9,421,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,952 duplication rate = 6.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3135 >>>>>>> ACTG content number of A's = 2,468,726 bp (26.2%) number of C's = 1,764,147 bp (18.73%) number of T's = 3,053,479 bp (32.41%) number of G's = 2,134,223 bp (22.65%) number of N's = 554 bp (0.01%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 97,757 number of insertions = 948 mapped reads with insertion percentage = 0.63% number of deletions = 2,570 mapped reads with deletion percentage = 1.72% homopolymer indels = 39.74% >>>>>>> Coverage mean coverageData = 0.003X std coverageData = 0.1783X There is a 0.25% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 858902 0.00344593725204801 0.41080831348758284 chr2 243199373 674109 0.0027718369158788907 0.26635793514287326 chr3 198022430 837138 0.004227490794855916 0.23561277011487602 chr4 191154276 410612 0.002148065994610552 0.12725191379448028 chr5 180915260 573671 0.0031709375980776854 0.07475780056128337 chr6 171115067 578567 0.003381157545875256 0.0896448991771875 chr7 159138663 580582 0.0036482774773594776 0.16431245594467125 chr8 146364022 497321 0.0033978363890546817 0.08951695019520481 chr9 141213431 385348 0.002728833916654854 0.08387427037491169 chr10 135534747 402859 0.0029723669311161956 0.07357966199846985 chr11 135006516 381285 0.002824197018757228 0.07084116522616746 chr12 133851895 326917 0.0024423785707329733 0.1543969506596499 chr13 115169878 371850 0.0032287088122121654 0.07361771718830006 chr14 107349540 357539 0.003330605794864142 0.07308073822899516 chr15 102531392 228030 0.0022240017964449367 0.06378236550336265 chr16 90354753 292051 0.0032322704705971582 0.09550525714585406 chr17 81195210 282190 0.003475451322805865 0.11525082553480703 chr18 78077248 220811 0.0028281094128727487 0.19875073105294827 chr19 59128983 241046 0.00407661332514378 0.08589705793684314 chr20 63025520 201379 0.0031951977548142405 0.0669872737617609 chr21 48129895 184228 0.003827724951404943 0.15959337641014182 chr22 51304566 122351 0.0023847974856662855 0.18190375008887624 chrMT 16571 13838 0.8350733208617465 1.2919897763024306 chrX 155270560 373720 0.0024068954217721632 0.08890518557193917 chrY 59373566 29003 4.884833765922027E-4 0.030574068588536327