BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094149.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 428,922 number of mapped reads = 414,731 (96.69%) number of supplementary alignments = 14,195 (3.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 208,389 number of mapped paired reads (second in pair) = 206,342 number of mapped paired reads (both in pair) = 411,768 number of mapped paired reads (singletons) = 2,963 number of mapped bases = 55,694,125 bp number of sequenced bases = 54,284,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 395,129 duplication rate = 49.34% >>>>>>> Insert size mean insert size = 359,705.2492 std insert size = 5,445,938.6502 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 40.2185 >>>>>>> ACTG content number of A's = 13,946,107 bp (25.69%) number of C's = 13,122,387 bp (24.17%) number of T's = 13,363,980 bp (24.62%) number of G's = 13,851,243 bp (25.52%) number of N's = 525 bp (0%) GC percentage = 49.69% >>>>>>> Mismatches and indels general error rate = 0.0421 number of mismatches = 2,252,092 number of insertions = 29,244 mapped reads with insertion percentage = 6.96% number of deletions = 176,053 mapped reads with deletion percentage = 40.52% homopolymer indels = 27.57% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 4.821X 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 446179 0.0017900817988333116 0.6354252939303916 chr2 243199373 2783526 0.011445448915692723 4.992107293577253 chr3 198022430 1206859 0.006094557066085898 2.396140799390723 chr4 191154276 746931 0.003907477329986591 1.5684920983964161 chr5 180915260 515503 0.0028494169038034713 1.2597837173730577 chr6 171115067 1204409 0.007038591172102922 3.547831946923622 chr7 159138663 1368188 0.008597458180228647 3.506238860790294 chr8 146364022 782664 0.005347379699636841 1.9950380837526271 chr9 141213431 528984 0.003745989289078317 1.3958417430495127 chr10 135534747 903512 0.006666275770596303 2.0564493581640373 chr11 135006516 1577070 0.011681436176013905 3.4507230546156444 chr12 133851895 1757211 0.013128024821762889 5.3809209623824295 chr13 115169878 940727 0.008168168763710942 2.4188841644781185 chr14 107349540 300218 0.002796639836556356 1.4204225969378856 chr15 102531392 1304801 0.012725868385752532 3.3343022647627736 chr16 90354753 448656 0.004965494178264203 1.5083369193820269 chr17 81195210 1280530 0.01577100422549557 4.298329261030271 chr18 78077248 152528 0.0019535524612752744 0.5527201147326986 chr19 59128983 383170 0.006480239986539258 1.9472860843035322 chr20 63025520 453494 0.007195402751139539 2.5544799467908805 chr21 48129895 958059 0.019905694786992573 8.406039701715311 chr22 51304566 96804 0.0018868496032107551 0.38135840763073026 chrMT 16571 1188707 71.73417415967654 422.9214143786098 chrX 155270560 33751591 0.21737276532009675 16.372843275318257 chrY 59373566 613804 0.010338001258000908 2.552281257445134