BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714261.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 438,034 number of mapped reads = 26,403 (6.03%) number of supplementary alignments = 565 (0.13%) number of secondary alignments = 0 number of mapped bases = 2,350,136 bp number of sequenced bases = 2,325,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,773 duplication rate = 35.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 20.9997 >>>>>>> ACTG content number of A's = 318,397 bp (13.69%) number of C's = 204,722 bp (8.81%) number of T's = 268,299 bp (11.54%) number of G's = 1,533,552 bp (65.96%) number of N's = 77 bp (0%) GC percentage = 74.76% >>>>>>> Mismatches and indels general error rate = 0.035 number of mismatches = 69,083 number of insertions = 2,664 mapped reads with insertion percentage = 7.75% number of deletions = 4,014 mapped reads with deletion percentage = 14.79% homopolymer indels = 36.84% >>>>>>> Coverage mean coverageData = 0.0008X std coverageData = 1.5564X There is a 0% of reference with a coverageData >= 1X There is a 0% 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 59623 2.392090329034727E-4 0.12332452008420533 chr2 243199373 1447717 0.00595279906416535 5.5343649860353485 chr3 198022430 56303 2.8432637656249343E-4 0.105972210447116 chr4 191154276 22239 1.1634058345626545E-4 0.06730459921685653 chr5 180915260 56521 3.1241698461478596E-4 0.12329164022544714 chr6 171115067 23780 1.3897081313125979E-4 0.060943436092581835 chr7 159138663 50133 3.150271533951495E-4 0.21717456032387641 chr8 146364022 24233 1.6556664451322607E-4 0.07515764265959189 chr9 141213431 29248 2.0711910894651372E-4 0.11288033465816623 chr10 135534747 26458 1.9521193336495475E-4 0.13541735094872656 chr11 135006516 59045 4.3734926097937376E-4 0.14661114606778822 chr12 133851895 71901 5.371683381845285E-4 0.18108641238227563 chr13 115169878 33741 2.9296722880960244E-4 0.10929747658602142 chr14 107349540 14317 1.3336806100892467E-4 0.06679523622094734 chr15 102531392 9197 8.969935763673237E-5 0.043262942507677725 chr16 90354753 2525 2.7945403159920098E-5 0.009730446162748768 chr17 81195210 6152 7.576801636451215E-5 0.049211784312005236 chr18 78077248 31185 3.994121309193685E-4 0.12109871020693266 chr19 59128983 9669 1.635238678128457E-4 0.07471725019044198 chr20 63025520 18465 2.9297655933659887E-4 0.11966463879753497 chr21 48129895 10178 2.114693996319751E-4 0.07450040952417812 chr22 51304566 16210 3.159562835011605E-4 0.12339018885950113 chrMT 16571 3107 0.1874962283507332 1.4268771723501035 chrX 155270560 266993 0.0017195339541507418 0.3024988326548821 chrY 59373566 1196 2.014364439555475E-5 0.008809647535367124