BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867836.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 = 20,381,577 number of mapped reads = 19,570,451 (96.02%) number of supplementary alignments = 97,992 (0.48%) number of secondary alignments = 0 number of mapped bases = 1,708,649,184 bp number of sequenced bases = 1,708,214,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,174,999 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2901 >>>>>>> ACTG content number of A's = 484,048,477 bp (28.34%) number of C's = 367,173,071 bp (21.49%) number of T's = 494,088,655 bp (28.92%) number of G's = 362,528,933 bp (21.22%) number of N's = 375,862 bp (0.02%) GC percentage = 42.72% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 8,677,395 number of insertions = 171,125 mapped reads with insertion percentage = 0.86% number of deletions = 167,873 mapped reads with deletion percentage = 0.83% homopolymer indels = 33.68% >>>>>>> Coverage mean coverageData = 0.5519X std coverageData = 6.9692X There is a 37.66% of reference with a coverageData >= 1X There is a 10.84% of reference with a coverageData >= 2X There is a 2.64% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 138523700 0.5557607015952029 12.489433965158781 chr2 243199373 152239172 0.6259850513677105 4.36878629848503 chr3 198022430 110615123 0.5585989577039329 4.314911643024296 chr4 191154276 107714323 0.5634941851889308 5.319886101529591 chr5 180915260 95891846 0.530037355610577 0.8787508854823106 chr6 171115067 91394097 0.5341089981281426 2.1672173733702285 chr7 159138663 86701650 0.5448182633028656 5.7141536538145825 chr8 146364022 104902508 0.7167233215277454 2.9820864252789043 chr9 141213431 69781399 0.4941555382221398 2.813417277859597 chr10 135534747 97753590 0.7212437560384423 21.632638933636787 chr11 135006516 69747517 0.5166233383876079 2.2259198851590387 chr12 133851895 74250754 0.5547232185244744 1.085818096427737 chr13 115169878 49234131 0.42749138798254177 0.7241600777406283 chr14 107349540 51330083 0.4781583880098601 0.9926805365678547 chr15 102531392 44367640 0.43272249732062545 0.7417314024228596 chr16 90354753 67571891 0.7478509846626441 12.333505991944973 chr17 81195210 54134452 0.6667197732477076 2.4051746728623558 chr18 78077248 43337371 0.5550576142232881 5.809388396332183 chr19 59128983 33846754 0.57242239393835 8.039582284405922 chr20 63025520 37032144 0.5875737955037896 1.7530777520083496 chr21 48129895 21540813 0.44755578627379095 3.7667163287950896 chr22 51304566 23604212 0.46008014179478685 0.8904582748391032 chrMT 16571 2223816 134.19926377406313 58.216752507402596 chrX 155270560 73653579 0.47435636865095354 1.5538260328190263 chrY 59373566 7256619 0.1222196928511924 6.299126337130003