BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081216.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,739,945 number of mapped reads = 2,384,153 (87.01%) number of supplementary alignments = 26,606 (0.97%) number of secondary alignments = 0 number of mapped bases = 151,148,696 bp number of sequenced bases = 151,095,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,637 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.309 >>>>>>> ACTG content number of A's = 43,629,985 bp (28.88%) number of C's = 29,712,734 bp (19.66%) number of T's = 45,345,744 bp (30.01%) number of G's = 32,387,986 bp (21.44%) number of N's = 19,311 bp (0.01%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,363,666 number of insertions = 11,179 mapped reads with insertion percentage = 0.46% number of deletions = 32,741 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.3562X There is a 4.01% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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% 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 13992591 0.056138640473036176 0.6331652441509824 chr2 243199373 8597038 0.03534975396503181 0.378330527628481 chr3 198022430 12432079 0.06278116574975875 0.29729357879208074 chr4 191154276 6099430 0.031908415169326375 0.21298989145016414 chr5 180915260 10940860 0.0604750533481808 0.2906299620814487 chr6 171115067 10542252 0.061609139305073585 0.32941188776090596 chr7 159138663 8308871 0.05221151694607363 0.44121229047973687 chr8 146364022 7181953 0.04906911481292855 0.3656479462366158 chr9 141213431 3830544 0.02712591835545728 0.25908314167874685 chr10 135534747 4724615 0.0348590682801068 0.31211752977679447 chr11 135006516 7808044 0.05783457148097948 0.3635369416619798 chr12 133851895 4189369 0.03129854082379633 0.20953411654680615 chr13 115169878 3711672 0.03222780178685263 0.2104730244038809 chr14 107349540 7200866 0.06707868519976891 0.3101088225887784 chr15 102531392 2302428 0.022455834794479334 0.19143774934611854 chr16 90354753 5330876 0.05899939762991771 0.29939617559016174 chr17 81195210 2581480 0.03179350111909311 0.22483882787661044 chr18 78077248 3643327 0.046663107285748594 0.43937695859775344 chr19 59128983 4359545 0.07372940948434713 0.5433396614773752 chr20 63025520 3738833 0.059322525224702626 0.2874082337169507 chr21 48129895 2412350 0.050121655158399996 0.27334594800897705 chr22 51304566 1118625 0.021803614906322374 0.17075374415567457 chrMT 16571 33331 2.0114054673827773 2.070698141470341 chrX 155270560 15617934 0.10058528802884462 0.3986085277565598 chrY 59373566 449783 0.007575475591275754 0.11892828766707379