BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525043.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 = 531,795 number of mapped reads = 490,682 (92.27%) number of supplementary alignments = 2,053 (0.39%) number of secondary alignments = 0 number of mapped bases = 29,116,374 bp number of sequenced bases = 29,106,680 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,004 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4714 >>>>>>> ACTG content number of A's = 7,741,285 bp (26.6%) number of C's = 5,385,579 bp (18.5%) number of T's = 9,355,575 bp (32.14%) number of G's = 6,621,698 bp (22.75%) number of N's = 2,543 bp (0.01%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 140,756 number of insertions = 2,460 mapped reads with insertion percentage = 0.5% number of deletions = 6,170 mapped reads with deletion percentage = 1.25% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.0094X std coverageData = 0.1238X There is a 0.87% of reference with a coverageData >= 1X There is a 0.05% 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 2323634 0.009322480283810407 0.1787304699357676 chr2 243199373 2467285 0.010145112504052384 0.1412615479428573 chr3 198022430 1960642 0.00990111069740938 0.10541603946539675 chr4 191154276 1923707 0.01006363572008193 0.11464454550637601 chr5 180915260 1773306 0.009801859721507185 0.10523177093338364 chr6 171115067 1658660 0.009693243436009058 0.10711241357808202 chr7 159138663 1578725 0.009920436493801634 0.12911621264791914 chr8 146364022 1507499 0.010299655471342541 0.16898350022491218 chr9 141213431 1226950 0.008688621126980479 0.10830405186486043 chr10 135534747 1417359 0.010457532340396813 0.13171976587031348 chr11 135006516 1330312 0.0098536873583198 0.1137281547320214 chr12 133851895 1304363 0.009744822813304212 0.10576533942965326 chr13 115169878 908124 0.007885082590779509 0.0938174251978201 chr14 107349540 856211 0.007975916804114858 0.09498574514454614 chr15 102531392 829488 0.0080900881556353 0.09539196063717029 chr16 90354753 821479 0.009091707660359605 0.10374835135854076 chr17 81195210 758895 0.00934654889124617 0.10430478929590316 chr18 78077248 774179 0.009915551839122199 0.15337881865971784 chr19 59128983 554703 0.00938123694770803 0.14696619531904903 chr20 63025520 620821 0.009850311429401931 0.1073766238186521 chr21 48129895 390179 0.008106791007958775 0.1026847933749018 chr22 51304566 349685 0.006815865083041536 0.08706497591526956 chrMT 16571 13841 0.8352543600265524 1.1250065183724833 chrX 155270560 1661578 0.010701178639402086 0.11341485368453817 chrY 59373566 104749 0.0017642362933026458 0.07167056264638316