BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716919.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 = 831,386 number of mapped reads = 697,884 (83.94%) number of supplementary alignments = 2,824 (0.34%) number of secondary alignments = 0 number of mapped bases = 38,558,846 bp number of sequenced bases = 38,548,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,947 duplication rate = 1.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.579 >>>>>>> ACTG content number of A's = 9,192,103 bp (23.85%) number of C's = 8,471,772 bp (21.98%) number of T's = 11,114,109 bp (28.83%) number of G's = 9,769,329 bp (25.34%) number of N's = 964 bp (0%) GC percentage = 47.32% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 206,264 number of insertions = 2,667 mapped reads with insertion percentage = 0.38% number of deletions = 6,201 mapped reads with deletion percentage = 0.88% homopolymer indels = 34.48% >>>>>>> Coverage mean coverageData = 0.0125X std coverageData = 0.1317X There is a 1.15% of reference with a coverageData >= 1X There is a 0.07% 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 3916122 0.015711583723596823 0.15628778773851434 chr2 243199373 3180160 0.013076349501937245 0.1506396812601275 chr3 198022430 2462479 0.012435353914200527 0.1215107500279179 chr4 191154276 2349095 0.012289000534835014 0.13054703167243153 chr5 180915260 2336187 0.012913156137298756 0.12104012117109042 chr6 171115067 1733102 0.010128284027729714 0.1084001054481662 chr7 159138663 2120255 0.013323317916778024 0.13837128258446252 chr8 146364022 2444569 0.016701980217515476 0.1433934013729931 chr9 141213431 1629185 0.011537039985948645 0.12115319359421708 chr10 135534747 2010761 0.014835760161193203 0.18230271206523052 chr11 135006516 1601771 0.011864397715440638 0.13201229924039146 chr12 133851895 1810630 0.013527115174574106 0.12427778529943058 chr13 115169878 782986 0.006798531122868777 0.08934694944710647 chr14 107349540 1177574 0.010969530004506773 0.11286985342883199 chr15 102531392 800386 0.007806253132699105 0.0950804690369648 chr16 90354753 1058980 0.01172024674783849 0.1218495737333945 chr17 81195210 1693693 0.020859518683429723 0.1595077489618392 chr18 78077248 989167 0.012669081266798748 0.13872594790607093 chr19 59128983 1073453 0.01815443029013369 0.1600202413754365 chr20 63025520 972253 0.015426338410218591 0.13784474172921862 chr21 48129895 638362 0.013263315866365385 0.1348000978168653 chr22 51304566 437593 0.008529318813456097 0.10032908207066978 chrMT 16571 30630 1.8484098726691207 1.900476137809166 chrX 155270560 1177977 0.0075866088201137424 0.09724235199495755 chrY 59373566 131476 0.0022143861124999634 0.07611485855811091