BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081111.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 = 2,433,123 number of mapped reads = 2,214,603 (91.02%) number of supplementary alignments = 12,499 (0.51%) number of secondary alignments = 0 number of mapped bases = 148,693,161 bp number of sequenced bases = 148,631,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,201 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8932 >>>>>>> ACTG content number of A's = 40,339,970 bp (27.14%) number of C's = 28,706,515 bp (19.31%) number of T's = 45,395,742 bp (30.54%) number of G's = 34,188,140 bp (23%) number of N's = 1,631 bp (0%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,307,553 number of insertions = 11,211 mapped reads with insertion percentage = 0.5% number of deletions = 33,961 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.048X std coverageData = 0.4266X There is a 4.03% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% 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 13512840 0.054213866933555205 0.739668023644681 chr2 243199373 9984416 0.04105444794876178 0.46928354299467845 chr3 198022430 12886665 0.06507679458332069 0.2950216014635864 chr4 191154276 9037189 0.04727693875914133 0.28276295218044856 chr5 180915260 8231773 0.04550071121695318 0.24709522499291087 chr6 171115067 11928243 0.06970889945068368 0.45225872766792874 chr7 159138663 3859691 0.024253634705979653 0.28746895233620834 chr8 146364022 11009952 0.07522307633770818 0.4441592141404127 chr9 141213431 7422412 0.052561657538085026 0.5398589668843254 chr10 135534747 7424498 0.05477929582146193 0.4207985417020827 chr11 135006516 6926973 0.05130843462399993 0.38097976236749065 chr12 133851895 7668665 0.05729216609148492 0.30157254279834345 chr13 115169878 3658269 0.031764112835128644 0.20229283375086302 chr14 107349540 3946446 0.03676257951361506 0.32946198743606264 chr15 102531392 4032213 0.039326619109979505 0.23536322565287995 chr16 90354753 3937397 0.0435770877487762 0.32480621847940727 chr17 81195210 3732639 0.04597117243738886 0.2589968374389286 chr18 78077248 3829999 0.04905397024239379 0.9768332920637527 chr19 59128983 3856503 0.0652218726643751 0.5767960073594655 chr20 63025520 2575830 0.040869635030381345 0.2630310752104141 chr21 48129895 2893448 0.0601174799986578 0.3589512828251241 chr22 51304566 1597041 0.03112863287840696 0.19972290801515255 chrMT 16571 80986 4.887212600325871 3.477586450077243 chrX 155270560 4276514 0.02754233642230697 0.23867845473496652 chrY 59373566 382559 0.006443254562139657 0.18378740989558182