BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094036.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 = 475,470 number of mapped reads = 437,886 (92.1%) number of supplementary alignments = 25,005 (5.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 220,074 number of mapped paired reads (second in pair) = 217,812 number of mapped paired reads (both in pair) = 429,540 number of mapped paired reads (singletons) = 8,346 number of mapped bases = 56,555,487 bp number of sequenced bases = 55,614,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 412,139 duplication rate = 43.06% >>>>>>> Insert size mean insert size = 414,884.721 std insert size = 6,024,303.282 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 43.3055 >>>>>>> ACTG content number of A's = 15,766,744 bp (28.35%) number of C's = 12,210,008 bp (21.95%) number of T's = 14,988,119 bp (26.95%) number of G's = 12,649,564 bp (22.74%) number of N's = 483 bp (0%) GC percentage = 44.7% >>>>>>> Mismatches and indels general error rate = 0.0338 number of mismatches = 1,824,417 number of insertions = 28,530 mapped reads with insertion percentage = 6.32% number of deletions = 133,904 mapped reads with deletion percentage = 29.55% homopolymer indels = 28.49% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 8.0175X There is a 0.04% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 1113773 0.004468486359357957 1.1687497014479953 chr2 243199373 2486376 0.010223611884065177 2.596515243266791 chr3 198022430 1101176 0.005560864998980166 2.0988981948975716 chr4 191154276 1268961 0.006638412838852739 2.346912829900953 chr5 180915260 452639 0.0025019393057279966 0.6542339374886761 chr6 171115067 786600 0.004596906711902816 1.2859876574796816 chr7 159138663 1787460 0.0112320913491651 3.582103653156301 chr8 146364022 780390 0.005331843094609685 1.2325693951180134 chr9 141213431 783995 0.005551844427602641 0.9981571960761754 chr10 135534747 616779 0.004550707576116994 0.871052322612957 chr11 135006516 1395076 0.010333397537641812 2.0800732544764275 chr12 133851895 1718498 0.012838802170114962 3.898388350652346 chr13 115169878 1874388 0.016274984679587833 4.422919178829792 chr14 107349540 357626 0.003331416231499455 1.1050102679858533 chr15 102531392 773460 0.007543640878298034 2.5839500226083127 chr16 90354753 400310 0.0044304254807713325 0.7582113666068679 chr17 81195210 916356 0.011285838167054436 2.08972094664226 chr18 78077248 183068 0.002344703542829788 0.7707068399849915 chr19 59128983 266789 0.0045119835732672755 0.6450684922670261 chr20 63025520 197510 0.003133809923345337 0.8853638189047981 chr21 48129895 288834 0.006001135053380025 1.7011206838763568 chr22 51304566 226232 0.004409588027701083 0.4285332589820472 chrMT 16571 11365939 685.8933679319292 2926.2979931678933 chrX 155270560 24835763 0.1599515259042023 15.192323948951675 chrY 59373566 577489 0.009726365433398425 2.352915334370412