BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093977.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 = 658,936 number of mapped reads = 532,544 (80.82%) number of supplementary alignments = 6,272 (0.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 266,972 number of mapped paired reads (second in pair) = 265,572 number of mapped paired reads (both in pair) = 527,484 number of mapped paired reads (singletons) = 5,060 number of mapped bases = 72,504,312 bp number of sequenced bases = 71,571,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 521,317 duplication rate = 32.36% >>>>>>> Insert size mean insert size = 107,840.7214 std insert size = 3,463,594.7175 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 31.1285 >>>>>>> ACTG content number of A's = 19,058,472 bp (26.63%) number of C's = 16,603,287 bp (23.2%) number of T's = 19,768,684 bp (27.62%) number of G's = 16,140,236 bp (22.55%) number of N's = 843 bp (0%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.039 number of mismatches = 1,921,013 number of insertions = 87,930 mapped reads with insertion percentage = 16.26% number of deletions = 203,657 mapped reads with deletion percentage = 36.89% homopolymer indels = 30.09% >>>>>>> Coverage mean coverageData = 0.0234X std coverageData = 26.9724X 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% 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 2279215 0.009144270095920844 4.853416586472757 chr2 243199373 1732571 0.007124076754918278 4.416030488922807 chr3 198022430 267325 0.0013499733338289 0.5107499359609218 chr4 191154276 222663 0.001164834000365234 0.3577435314272796 chr5 180915260 807286 0.004462232760243663 2.6845654120981983 chr6 171115067 4324650 0.025273344281249062 17.547164887379637 chr7 159138663 11787433 0.07407020253777047 42.635858117469645 chr8 146364022 229094 0.0015652343852644334 0.4600762495369689 chr9 141213431 2907106 0.020586611198477288 16.937867966622857 chr10 135534747 2064419 0.015231658638799097 13.589075561782424 chr11 135006516 12883155 0.09542617187454863 68.9286195547977 chr12 133851895 336404 0.0025132554156218705 0.8168871612775415 chr13 115169878 186374 0.001618252994936749 0.9832812653241099 chr14 107349540 299664 0.0027914791251085007 1.3596189682129998 chr15 102531392 834228 0.008136317899595081 5.784137453926293 chr16 90354753 1212549 0.01341986956679523 5.624040364313227 chr17 81195210 314614 0.003874785224399321 0.8788867999693551 chr18 78077248 31794 4.0721209845920797E-4 0.055761154703573415 chr19 59128983 271542 0.004592367164508816 1.0560704591916366 chr20 63025520 165708 0.0026292206712455525 0.6318157901750161 chr21 48129895 33909 7.045309365416234E-4 0.1528591525886404 chr22 51304566 93658 0.0018255295249939353 0.4264601644804329 chrMT 16571 8646 0.5217548729708527 4.106530245191947 chrX 155270560 29195274 0.1880283937921007 87.3351076055805 chrY 59373566 15031 2.5315979841938413E-4 0.1043127932145221