BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525025.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 = 1,617,744 number of mapped reads = 1,489,469 (92.07%) number of supplementary alignments = 5,861 (0.36%) number of secondary alignments = 0 number of mapped bases = 87,908,979 bp number of sequenced bases = 87,879,173 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,620 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8008 >>>>>>> ACTG content number of A's = 22,846,502 bp (26%) number of C's = 17,398,637 bp (19.8%) number of T's = 27,191,892 bp (30.94%) number of G's = 20,441,235 bp (23.26%) number of N's = 907 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 429,314 number of insertions = 6,319 mapped reads with insertion percentage = 0.42% number of deletions = 17,802 mapped reads with deletion percentage = 1.18% homopolymer indels = 41.99% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 0.257X There is a 2.57% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% 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 6981747 0.028010951274620898 0.463183733234801 chr2 243199373 7407056 0.030456723258081755 0.27982391715011273 chr3 198022430 5814795 0.029364325041360214 0.1847930888205215 chr4 191154276 5650183 0.029558234941079738 0.21271049649050597 chr5 180915260 5310472 0.02935336687463512 0.1854470512343402 chr6 171115067 5104733 0.029832165510007367 0.2300915984738197 chr7 159138663 4730121 0.029723267186177127 0.2889649018928718 chr8 146364022 4520634 0.03088623787613598 0.2770052114051414 chr9 141213431 3702874 0.02622182588283688 0.21089480924258788 chr10 135534747 4289744 0.031650510994055275 0.28595982042298607 chr11 135006516 4139293 0.030659949776053772 0.2449767048620688 chr12 133851895 3958456 0.029573402752348033 0.18844241616886984 chr13 115169878 2656195 0.0230632787507164 0.16483121070307705 chr14 107349540 2696116 0.025115300913259617 0.1765848588687416 chr15 102531392 2504068 0.02442245200377266 0.1722364547701181 chr16 90354753 2606393 0.02884621908047272 0.19555908702319766 chr17 81195210 2375649 0.029258487046218612 0.2055148060586046 chr18 78077248 2357565 0.030195288133106332 0.3714067534144633 chr19 59128983 1855368 0.03137831746573419 0.3153498198541578 chr20 63025520 1893867 0.030049208638024724 0.19248539610886845 chr21 48129895 1174092 0.024394235640863127 0.1957136558576349 chr22 51304566 1062113 0.020702114505753738 0.1551995848845717 chrMT 16571 1714 0.10343370949248687 0.34310141645923997 chrX 155270560 4840357 0.03117369448529071 0.20724826741423139 chrY 59373566 275374 0.0046379899095162986 0.15370919393774282