BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716877.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 = 660,595 number of mapped reads = 584,467 (88.48%) number of supplementary alignments = 1,259 (0.19%) number of secondary alignments = 0 number of mapped bases = 33,293,613 bp number of sequenced bases = 33,283,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,256 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0169 >>>>>>> ACTG content number of A's = 8,240,701 bp (24.76%) number of C's = 5,815,670 bp (17.47%) number of T's = 10,584,768 bp (31.8%) number of G's = 8,641,586 bp (25.96%) number of N's = 362 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 166,928 number of insertions = 2,206 mapped reads with insertion percentage = 0.38% number of deletions = 6,475 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1273X There is a 1.02% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 4000340 0.01604946853873636 0.17215921591296787 chr2 243199373 2677076 0.01100774219512482 0.16071126837115965 chr3 198022430 2166684 0.01094160898843631 0.10927688824474888 chr4 191154276 1434713 0.007505523967457573 0.09200970685817135 chr5 180915260 2429107 0.01342676676362182 0.12044654972872844 chr6 171115067 1263723 0.007385223418110809 0.0963607257829611 chr7 159138663 2296285 0.01442946017461514 0.18999933371378874 chr8 146364022 1527225 0.010434429029286993 0.11439516860589756 chr9 141213431 934411 0.00661701223023184 0.09820548022481372 chr10 135534747 1566371 0.011556969962839123 0.14330681413487006 chr11 135006516 1450525 0.010744111047203084 0.11874336882473988 chr12 133851895 1361915 0.010174790577301876 0.1051752467144143 chr13 115169878 988973 0.008587080382250643 0.09635111342014895 chr14 107349540 738016 0.006874887400542191 0.0879498939041341 chr15 102531392 1459410 0.014233787053237315 0.12489034318751135 chr16 90354753 1033365 0.0114367530837033 0.11645552192800065 chr17 81195210 1261785 0.015540140853136533 0.13351944575510286 chr18 78077248 1088746 0.013944472018276054 0.16933505831005086 chr19 59128983 549701 0.009296642223662126 0.13758677098075986 chr20 63025520 882267 0.013998567564377097 0.12332049728584496 chr21 48129895 443797 0.009220817955243824 0.10166912495662678 chr22 51304566 397589 0.007749583146264213 0.09152129177951186 chrMT 16571 214 0.012914127089493695 0.1129041735765782 chrX 155270560 1265472 0.008150109074121972 0.10076286535711042 chrY 59373566 75903 0.0012783971911001606 0.044042438311953126