BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524312.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 = 707,815 number of mapped reads = 646,288 (91.31%) number of supplementary alignments = 2,603 (0.37%) number of secondary alignments = 0 number of mapped bases = 37,647,852 bp number of sequenced bases = 37,638,309 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,689 duplication rate = 1.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.885 >>>>>>> ACTG content number of A's = 8,851,883 bp (23.52%) number of C's = 6,886,018 bp (18.3%) number of T's = 12,240,636 bp (32.52%) number of G's = 9,654,909 bp (25.65%) number of N's = 4,863 bp (0.01%) GC percentage = 43.95% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 190,916 number of insertions = 2,613 mapped reads with insertion percentage = 0.4% number of deletions = 5,981 mapped reads with deletion percentage = 0.92% homopolymer indels = 40.41% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.1423X There is a 1.15% of reference with a coverageData >= 1X There is a 0.04% 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 3222249 0.01292774712886272 0.23312687212062017 chr2 243199373 2455000 0.010094598393557535 0.1641864264659697 chr3 198022430 2583410 0.01304604735938247 0.1188636922843363 chr4 191154276 1963545 0.01027204329972718 0.11039323804532888 chr5 180915260 2213856 0.012236977687785984 0.11432919635046807 chr6 171115067 2426898 0.014182842239134909 0.1270937084448251 chr7 159138663 1699148 0.010677153923305238 0.1544687079313078 chr8 146364022 3876175 0.026483113452566917 0.18711510959094307 chr9 141213431 1553657 0.011002190011232005 0.12134481972875061 chr10 135534747 1928929 0.01423198879029892 0.14821104024918125 chr11 135006516 1793155 0.013281988552315504 0.13171234143014504 chr12 133851895 1476646 0.011031939443218192 0.10904577741376326 chr13 115169878 925288 0.008034114614586984 0.09264429901792053 chr14 107349540 778275 0.007249914624692383 0.09119496372676647 chr15 102531392 1168204 0.011393622745314918 0.11031246811847271 chr16 90354753 1213372 0.013428978108102403 0.1240361277403109 chr17 81195210 1197879 0.014753074719555502 0.13061940214280865 chr18 78077248 859663 0.011010416248277604 0.17730477174826773 chr19 59128983 698444 0.01181221060406197 0.1709829637755827 chr20 63025520 860991 0.013660990024358386 0.12175993934466663 chr21 48129895 544946 0.011322401596762262 0.11494056691150709 chr22 51304566 281854 0.005493741044413084 0.07651457522937073 chrMT 16571 3244 0.19576368354353993 0.48825034324595473 chrX 155270560 1814553 0.011686394381523451 0.11660505801318985 chrY 59373566 108471 0.0018269241231021899 0.06592579007253829