BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094067.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 = 325,858 number of mapped reads = 314,425 (96.49%) number of supplementary alignments = 10,701 (3.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 157,899 number of mapped paired reads (second in pair) = 156,526 number of mapped paired reads (both in pair) = 312,426 number of mapped paired reads (singletons) = 1,999 number of mapped bases = 42,487,617 bp number of sequenced bases = 41,638,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 297,225 duplication rate = 50.09% >>>>>>> Insert size mean insert size = 440,787.9292 std insert size = 6,094,499.1472 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 37.3619 >>>>>>> ACTG content number of A's = 10,976,031 bp (26.36%) number of C's = 9,803,866 bp (23.54%) number of T's = 10,580,347 bp (25.41%) number of G's = 10,278,187 bp (24.68%) number of N's = 479 bp (0%) GC percentage = 48.23% >>>>>>> Mismatches and indels general error rate = 0.0384 number of mismatches = 1,547,907 number of insertions = 23,763 mapped reads with insertion percentage = 7.42% number of deletions = 124,434 mapped reads with deletion percentage = 37.57% homopolymer indels = 26.03% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 3.733X There is a 0.01% 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% 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 387823 0.0015559560030143315 0.599818781840844 chr2 243199373 1839999 0.007565804867432779 3.226900183165405 chr3 198022430 955525 0.004825337210537211 2.155703904515152 chr4 191154276 373655 0.0019547300108525953 0.9033568519019616 chr5 180915260 255428 0.001411865422518808 0.6332909934604956 chr6 171115067 804763 0.004703051660553071 2.2294280368517008 chr7 159138663 1210185 0.007604594491283366 2.6936643979665575 chr8 146364022 1185363 0.008098732077750637 2.5332943370199463 chr9 141213431 534641 0.003786049217938767 1.4541672517173228 chr10 135534747 681256 0.005026430602331076 1.604446406268152 chr11 135006516 1316291 0.009749833111758843 2.6258477344529054 chr12 133851895 1029971 0.007694855571525528 2.945571918854498 chr13 115169878 1037043 0.00900446382343133 2.9058023575540197 chr14 107349540 232677 0.0021674708620083513 0.9115880943294885 chr15 102531392 663376 0.006469979457608456 2.1979510403635896 chr16 90354753 268921 0.00297627951016589 1.0298206483482866 chr17 81195210 1084227 0.013353336976405382 3.4933058440433915 chr18 78077248 100396 0.0012858547473394554 0.5595526337243846 chr19 59128983 186204 0.0031491155530275227 0.8534828925959919 chr20 63025520 153499 0.002435505490474335 0.6894294158836894 chr21 48129895 663957 0.013795105931562909 6.16047985621927 chr22 51304566 75161 0.0014649963124139867 0.333475771804864 chrMT 16571 1332118 80.38851004767365 387.94060738346406 chrX 155270560 25714058 0.16560807148502588 13.006886110527555 chrY 59373566 401080 0.006755194727566136 2.0045639897243808