BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714071.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 = 513,218 number of mapped reads = 126,060 (24.56%) number of supplementary alignments = 5,095 (0.99%) number of secondary alignments = 0 number of mapped bases = 14,922,535 bp number of sequenced bases = 14,655,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,907 duplication rate = 38.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.197 >>>>>>> ACTG content number of A's = 3,321,876 bp (22.67%) number of C's = 2,653,567 bp (18.11%) number of T's = 3,113,205 bp (21.24%) number of G's = 5,566,985 bp (37.98%) number of N's = 354 bp (0%) GC percentage = 56.09% >>>>>>> Mismatches and indels general error rate = 0.0413 number of mismatches = 555,384 number of insertions = 16,047 mapped reads with insertion percentage = 11.81% number of deletions = 45,657 mapped reads with deletion percentage = 33.72% homopolymer indels = 29.81% >>>>>>> Coverage mean coverageData = 0.0048X std coverageData = 3.7258X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 876260 0.0035155780013081694 1.196657655413436 chr2 243199373 3856921 0.015859091051192802 12.497317904382216 chr3 198022430 1077529 0.005441449233806493 2.642096725921367 chr4 191154276 524904 0.0027459704851174765 1.1841124216391823 chr5 180915260 687413 0.0037996407820987572 0.8291997135534575 chr6 171115067 339036 0.0019813334146665178 0.4976828724163422 chr7 159138663 521053 0.003274207475275823 1.3824354722691738 chr8 146364022 668523 0.004567536412739464 1.6772900203096492 chr9 141213431 287661 0.0020370654403262817 0.47185986854288786 chr10 135534747 432777 0.0031931073734176815 0.744265927794799 chr11 135006516 545114 0.004037686595808457 1.4243914481056623 chr12 133851895 495985 0.003705476115971313 1.0080897101933353 chr13 115169878 48555 4.2159461174387974E-4 0.0934468958950269 chr14 107349540 355412 0.0033107920164352823 0.9106145316631148 chr15 102531392 400347 0.0039046285453727186 1.0463896479790717 chr16 90354753 446110 0.004937316357889883 1.4070077698383592 chr17 81195210 692473 0.008528495708059625 2.592820639563911 chr18 78077248 169629 0.0021725791359859404 0.4736957434969631 chr19 59128983 709621 0.012001238039220123 2.457709339103578 chr20 63025520 221564 0.003515464846620861 0.6116142024689305 chr21 48129895 33332 6.925425455426403E-4 0.14171316440104464 chr22 51304566 196963 0.003839092996128259 1.2575548439207394 chrMT 16571 144291 8.707440709673525 58.41577583086713 chrX 155270560 1147154 0.0073880972671187635 0.8365113953626141 chrY 59373566 43908 7.395210184949982E-4 0.38258462024764794