BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094008.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 = 582,124 number of mapped reads = 467,749 (80.35%) number of supplementary alignments = 9,702 (1.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 234,378 number of mapped paired reads (second in pair) = 233,371 number of mapped paired reads (both in pair) = 463,806 number of mapped paired reads (singletons) = 3,943 number of mapped bases = 63,633,642 bp number of sequenced bases = 62,699,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 461,730 duplication rate = 40.35% >>>>>>> Insert size mean insert size = 114,654.729 std insert size = 2,906,607.7107 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 32.6716 >>>>>>> ACTG content number of A's = 17,701,369 bp (28.23%) number of C's = 13,836,453 bp (22.07%) number of T's = 16,901,540 bp (26.96%) number of G's = 14,259,795 bp (22.74%) number of N's = 607 bp (0%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0312 number of mismatches = 1,931,426 number of insertions = 17,843 mapped reads with insertion percentage = 3.7% number of deletions = 166,321 mapped reads with deletion percentage = 34.48% homopolymer indels = 33.15% >>>>>>> Coverage mean coverageData = 0.0206X std coverageData = 16.2388X 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% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 645914 0.0025914238344064144 1.3552119853507145 chr2 243199373 1808641 0.007436865390273847 4.154070683829403 chr3 198022430 663763 0.003351958664480584 1.6376477663143583 chr4 191154276 2007862 0.010503882215012549 6.877645314102028 chr5 180915260 3860370 0.02133800100665914 20.96774762490412 chr6 171115067 326111 0.0019057994466378581 0.8602680025278694 chr7 159138663 326677 0.0020527821073876937 0.7532064960614283 chr8 146364022 903890 0.006175629691291211 3.471290556084421 chr9 141213431 534130 0.003782430581974883 2.1383700861531625 chr10 135534747 1305342 0.009631050552667502 7.541083723004497 chr11 135006516 570565 0.00422620342265554 3.0652962925364506 chr12 133851895 2737324 0.020450394071746238 10.658655862010223 chr13 115169878 139946 0.0012151267538895892 0.6337501150046542 chr14 107349540 275803 0.0025692052336693757 1.0669500690870262 chr15 102531392 1404196 0.01369527880787964 7.620650586845545 chr16 90354753 254398 0.0028155464051791497 0.9557628014990183 chr17 81195210 162458 0.0020008323151082434 0.8063752446064977 chr18 78077248 94997 0.0012167052814156564 0.41564363509097624 chr19 59128983 159869 0.0027037332943812007 0.9095368350787341 chr20 63025520 23602 3.744832252078206E-4 0.060622744918351165 chr21 48129895 62531 0.001299213305992045 0.40172892018019335 chr22 51304566 329083 0.006414302383924269 2.490847551951597 chrMT 16571 16578518 1000.4536841470039 5077.654542167965 chrX 155270560 28424286 0.18306294509403456 39.74620456214975 chrY 59373566 33366 5.619672566070901E-4 0.22255232595751726