BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867865.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 = 1,861,673 number of mapped reads = 1,714,045 (92.07%) number of supplementary alignments = 7,836 (0.42%) number of secondary alignments = 0 number of mapped bases = 101,277,758 bp number of sequenced bases = 101,247,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,683 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8964 >>>>>>> ACTG content number of A's = 26,266,369 bp (25.94%) number of C's = 19,000,279 bp (18.77%) number of T's = 32,463,503 bp (32.06%) number of G's = 23,502,439 bp (23.21%) number of N's = 15,082 bp (0.01%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 507,389 number of insertions = 6,770 mapped reads with insertion percentage = 0.39% number of deletions = 18,974 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.5% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.3098X There is a 2.94% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8148033 0.032690121161222704 0.5755341424499728 chr2 243199373 8593414 0.03533485261082478 0.42280822623219344 chr3 198022430 6658079 0.03362285272431007 0.19905115689342165 chr4 191154276 6576722 0.03440530935337277 0.23118054280767064 chr5 180915260 6159945 0.034048786155463064 0.20236246242861836 chr6 171115067 5789983 0.03383678072019222 0.22685065323655282 chr7 159138663 5663464 0.03558823414269856 0.36164385498324453 chr8 146364022 5149699 0.03518418617930573 0.3243494647900334 chr9 141213431 4279222 0.030303222361334738 0.255686583125705 chr10 135534747 4936201 0.0364201882488481 0.31010800379680414 chr11 135006516 4561762 0.03378919873763723 0.261477910721993 chr12 133851895 4547924 0.033977285118003 0.20301368645321552 chr13 115169878 3175964 0.027576342487746666 0.18256562815089 chr14 107349540 3028721 0.028213637431515774 0.18999130091906635 chr15 102531392 2942466 0.028698196158304375 0.18476179460692538 chr16 90354753 2892938 0.03201755197095166 0.21594594875275305 chr17 81195210 2758730 0.03397651166860705 0.21430324852290758 chr18 78077248 2675429 0.03426643572273449 0.45781857833602063 chr19 59128983 2079350 0.035166341352429485 0.4278654281031326 chr20 63025520 2138566 0.03393174701295602 0.20303560467388526 chr21 48129895 1346722 0.027980987700056276 0.21225091543032318 chr22 51304566 1177643 0.02295396086188508 0.16476196718278346 chrMT 16571 34825 2.1015629714561586 1.9046754620088566 chrX 155270560 5624637 0.036224748593680606 0.22982439842953128 chrY 59373566 337319 0.005681299317612151 0.2095461853946562