BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716634.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 = 1,192,006 number of mapped reads = 1,031,511 (86.54%) number of supplementary alignments = 5,166 (0.43%) number of secondary alignments = 0 number of mapped bases = 59,597,648 bp number of sequenced bases = 59,581,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,466 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2224 >>>>>>> ACTG content number of A's = 14,350,323 bp (24.09%) number of C's = 11,410,837 bp (19.15%) number of T's = 18,847,872 bp (31.63%) number of G's = 14,971,707 bp (25.13%) number of N's = 763 bp (0%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 293,482 number of insertions = 3,778 mapped reads with insertion percentage = 0.36% number of deletions = 10,327 mapped reads with deletion percentage = 1% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 0.2167X There is a 1.77% of reference with a coverageData >= 1X There is a 0.11% 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 5507112 0.022094677148266764 0.4454232892489799 chr2 243199373 5627984 0.023141441240475565 0.2549029529896336 chr3 198022430 4236365 0.02139335932803168 0.1553813352746559 chr4 191154276 2779324 0.014539690443545191 0.13370462596957292 chr5 180915260 2671361 0.014765813563764605 0.13064172527349852 chr6 171115067 4175819 0.024403572830906817 0.19173453978186203 chr7 159138663 4595481 0.028877212572786286 0.29002212959886553 chr8 146364022 3329726 0.022749620805036362 0.1782899071974688 chr9 141213431 2318059 0.01641528701331533 0.16529475038981264 chr10 135534747 3121006 0.0230273495843837 0.19034023335043254 chr11 135006516 1943229 0.014393594158077526 0.15797824316546075 chr12 133851895 2283881 0.017062746851660187 0.1405901473560497 chr13 115169878 1293007 0.011226954672991838 0.11303217710900616 chr14 107349540 1312947 0.01223057872441745 0.12307040856502459 chr15 102531392 1740382 0.01697413802789296 0.14076768547560278 chr16 90354753 1379870 0.015271692458724334 0.13833900151174475 chr17 81195210 1292276 0.015915667931642764 0.13635598126810944 chr18 78077248 1964862 0.02516561546841405 0.2823904082937983 chr19 59128983 1472354 0.024900715779265135 0.30770840410387246 chr20 63025520 943515 0.014970364385728194 0.1311722684755119 chr21 48129895 719540 0.014949959894988344 0.13527134226085924 chr22 51304566 942788 0.018376298125200006 0.1444576820802744 chrMT 16571 112137 6.767062941282965 4.440892488886672 chrX 155270560 3698459 0.02381944780774926 0.18044415287222793 chrY 59373566 136164 0.0022933438089266863 0.06203164741220396