BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524804.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,409,027 number of mapped reads = 1,284,289 (91.15%) number of supplementary alignments = 5,500 (0.39%) number of secondary alignments = 0 number of mapped bases = 73,280,122 bp number of sequenced bases = 73,256,642 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,133 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.515 >>>>>>> ACTG content number of A's = 18,306,566 bp (24.99%) number of C's = 13,428,809 bp (18.33%) number of T's = 23,898,014 bp (32.62%) number of G's = 17,614,700 bp (24.05%) number of N's = 8,553 bp (0.01%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 371,411 number of insertions = 5,645 mapped reads with insertion percentage = 0.44% number of deletions = 14,398 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.96% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2225X There is a 2.11% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 5892564 0.02364112063736844 0.30980578608117015 chr2 243199373 6170794 0.025373396007891846 0.33558058708159594 chr3 198022430 4781475 0.02414612829465834 0.17211883900873057 chr4 191154276 4708858 0.02463380939487851 0.1977218332119018 chr5 180915260 4369936 0.024154601441580992 0.17083009581716352 chr6 171115067 4147749 0.024239531168812854 0.1887034154706334 chr7 159138663 4012138 0.02521158544608358 0.25593144068073453 chr8 146364022 3658644 0.024996880722504333 0.21174427257085093 chr9 141213431 3127703 0.022148764305570907 0.1888470763323724 chr10 135534747 3606468 0.026609176464541598 0.2730128567451982 chr11 135006516 3319334 0.024586472552184074 0.20143467757086603 chr12 133851895 3302829 0.024675250208448674 0.1740853890619723 chr13 115169878 2261860 0.019639336598064296 0.15462722495469924 chr14 107349540 2199820 0.02049212320798021 0.16140629683260657 chr15 102531392 2129414 0.020768410127505146 0.1598963593858918 chr16 90354753 2209232 0.02445064511437489 0.1886514258633227 chr17 81195210 2044497 0.025180019855851103 0.18213428920020366 chr18 78077248 1924647 0.024650548646386716 0.2891007049393076 chr19 59128983 1591240 0.02691133720327982 0.2468300058213595 chr20 63025520 1572978 0.02495779487420334 0.183231631572308 chr21 48129895 964912 0.02004808030435138 0.17356399308182013 chr22 51304566 906370 0.01766645877094058 0.14764430485503277 chrMT 16571 29549 1.783175426950697 1.65475747973611 chrX 155270560 4083715 0.02630063934850238 0.18846351175829928 chrY 59373566 263396 0.004436250300344096 0.13457136446911486