BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716665.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 = 2,117,457 number of mapped reads = 1,987,437 (93.86%) number of supplementary alignments = 38,965 (1.84%) number of secondary alignments = 0 number of mapped bases = 158,276,953 bp number of sequenced bases = 158,204,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,683 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5132 >>>>>>> ACTG content number of A's = 39,607,824 bp (25.04%) number of C's = 31,018,834 bp (19.61%) number of T's = 48,556,928 bp (30.69%) number of G's = 39,010,133 bp (24.66%) number of N's = 10,522 bp (0.01%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,003,679 number of insertions = 12,856 mapped reads with insertion percentage = 0.64% number of deletions = 36,974 mapped reads with deletion percentage = 1.83% homopolymer indels = 43.11% >>>>>>> Coverage mean coverageData = 0.0511X std coverageData = 0.4723X There is a 4.3% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15374122 0.061681378920215406 1.0045362829075133 chr2 243199373 12872825 0.05293116031183189 0.5182761707837117 chr3 198022430 9910059 0.05004513377600709 0.25383429553178766 chr4 191154276 9988739 0.052254855130732206 0.33481612571868435 chr5 180915260 9154137 0.050599031834019974 0.25758719186665674 chr6 171115067 8758458 0.051184610178132355 0.2840009170172876 chr7 159138663 8434614 0.053001664340990476 0.5617170442130087 chr8 146364022 7782467 0.05317199468596183 0.5159366715524253 chr9 141213431 6303937 0.04464119988699942 0.37610117725536824 chr10 135534747 7479516 0.05518522862627987 0.458413993789055 chr11 135006516 8814970 0.06529292260234314 0.507734266407503 chr12 133851895 6834321 0.05105882886454465 0.2587797549831404 chr13 115169878 5419620 0.04705761692306386 0.25004109979270395 chr14 107349540 4636301 0.04318882968664794 0.26233084494464554 chr15 102531392 4386283 0.04277990295889087 0.23461101533594844 chr16 90354753 3538077 0.039157619079540844 0.2512814229041106 chr17 81195210 4958937 0.06107425548871664 0.34932782789124833 chr18 78077248 4145314 0.05309247067724518 0.6738180680566583 chr19 59128983 3099992 0.05242762250789938 0.6893863681869737 chr20 63025520 3360724 0.05332322525859366 0.28385433970159807 chr21 48129895 2077642 0.043167391077832185 0.28471236475200934 chr22 51304566 1814168 0.03536075132182192 0.21419992564210083 chrMT 16571 101792 6.1427795546436545 4.265558587319547 chrX 155270560 8538394 0.05499042445650998 0.320305248281397 chrY 59373566 491544 0.008278835736428566 0.27596729317524604