BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063573.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 = 2,844,736 number of mapped reads = 2,588,186 (90.98%) number of supplementary alignments = 24,921 (0.88%) number of secondary alignments = 0 number of mapped bases = 173,342,604 bp number of sequenced bases = 173,265,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,066 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5632 >>>>>>> ACTG content number of A's = 51,247,599 bp (29.58%) number of C's = 32,076,592 bp (18.51%) number of T's = 54,583,815 bp (31.5%) number of G's = 35,352,241 bp (20.4%) number of N's = 5,032 bp (0%) GC percentage = 38.92% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,397,411 number of insertions = 12,325 mapped reads with insertion percentage = 0.47% number of deletions = 46,554 mapped reads with deletion percentage = 1.78% homopolymer indels = 46.13% >>>>>>> Coverage mean coverageData = 0.056X std coverageData = 0.47X There is a 4.15% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 8108049 0.03252970430914192 0.7461177308222018 chr2 243199373 22487206 0.09246407884447959 0.6301645550320577 chr3 198022430 17079039 0.08624800230963735 0.36947087620291247 chr4 191154276 3619633 0.01893566325453269 0.1837692167723583 chr5 180915260 3005144 0.016610782307694773 0.16495880709190552 chr6 171115067 40013216 0.2338380640671461 1.012549655838665 chr7 159138663 7544076 0.04740567664565587 0.3710047317573501 chr8 146364022 2616884 0.017879284568990596 0.5186958857119833 chr9 141213431 1918975 0.01358918189587788 0.2986160747399813 chr10 135534747 14223234 0.10494160585993495 0.5053986088611222 chr11 135006516 8259223 0.061176476845013913 0.3414979429202589 chr12 133851895 5630844 0.042067719698701316 0.2677558023891558 chr13 115169878 1901419 0.01650969014658503 0.1591751390777281 chr14 107349540 1969529 0.01834687880357941 0.17370540456059683 chr15 102531392 1436879 0.014014039719659711 0.14622666903653725 chr16 90354753 1198314 0.01326232389789168 0.15311329187919112 chr17 81195210 7105154 0.08750705860604338 0.3888485240298824 chr18 78077248 6469807 0.08286417830710427 0.5176398269909581 chr19 59128983 2305668 0.03899387209145809 0.545867976307568 chr20 63025520 4442780 0.07049176270183888 0.3363562261503759 chr21 48129895 2924230 0.06075704092020147 0.3189911776742181 chr22 51304566 609851 0.011886875721743753 0.1320342924719335 chrMT 16571 32490 1.9606541548488323 2.300309269318479 chrX 155270560 8103427 0.052189075636746594 0.31219336277845455 chrY 59373566 337533 0.005684903615187944 0.21554575214511285