BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094043.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 = 374,300 number of mapped reads = 355,064 (94.86%) number of supplementary alignments = 12,608 (3.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 178,418 number of mapped paired reads (second in pair) = 176,646 number of mapped paired reads (both in pair) = 352,498 number of mapped paired reads (singletons) = 2,566 number of mapped bases = 48,248,974 bp number of sequenced bases = 47,152,062 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 335,595 duplication rate = 49.05% >>>>>>> Insert size mean insert size = 485,825.3363 std insert size = 6,352,963.7189 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 41.1791 >>>>>>> ACTG content number of A's = 12,942,371 bp (27.45%) number of C's = 10,547,467 bp (22.37%) number of T's = 12,536,546 bp (26.59%) number of G's = 11,125,140 bp (23.59%) number of N's = 538 bp (0%) GC percentage = 45.96% >>>>>>> Mismatches and indels general error rate = 0.0419 number of mismatches = 1,922,600 number of insertions = 32,195 mapped reads with insertion percentage = 8.84% number of deletions = 150,648 mapped reads with deletion percentage = 39.29% homopolymer indels = 31.18% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 4.4344X 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% 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 649601 0.002606216174683071 0.8786909701947366 chr2 243199373 2487538 0.010228389856909706 3.560878836937602 chr3 198022430 927054 0.004681560568668913 1.7338768658584074 chr4 191154276 1670703 0.00874007652332088 3.2524361021439514 chr5 180915260 289902 0.0016024187235504622 0.4940931554077151 chr6 171115067 837915 0.004896792636033623 1.9650911344737079 chr7 159138663 1552121 0.009753261531423071 3.261544691084125 chr8 146364022 825265 0.0056384416656710895 2.754055531639059 chr9 141213431 705599 0.004996684770020211 2.0274090452734823 chr10 135534747 1077366 0.007949002184657489 3.3679977476278085 chr11 135006516 1041529 0.007714657268838787 2.068176644194766 chr12 133851895 1451283 0.01084245389278949 3.7026712758557374 chr13 115169878 1012218 0.008788912670377232 2.3817975100974524 chr14 107349540 258828 0.002411076936147095 1.0990741124817962 chr15 102531392 460605 0.004492331480294347 1.7302025304277455 chr16 90354753 372358 0.004121067100919417 1.6531286908802552 chr17 81195210 905899 0.011157049781631206 2.626246868399701 chr18 78077248 88552 0.001134158826909473 0.25385607647932634 chr19 59128983 409172 0.00691999048926649 2.67398163815995 chr20 63025520 294932 0.004679564722353738 1.0215704324399995 chr21 48129895 146962 0.0030534452651517314 0.8054820836200408 chr22 51304566 76926 0.001499398708489221 0.3208488693553364 chrMT 16571 4207248 253.89222135055218 1024.057531493555 chrX 155270560 26134055 0.16831300795205478 12.900175845061838 chrY 59373566 365343 0.006153293874920702 1.959376937920234