BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094121.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 = 565,676
number of mapped reads = 493,191 (87.19%)
number of supplementary alignments = 34,699 (6.13%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 247,170
number of mapped paired reads (second in pair) = 246,021
number of mapped paired reads (both in pair) = 489,772
number of mapped paired reads (singletons) = 3,419
number of mapped bases = 67,821,155 bp
number of sequenced bases = 67,561,829 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 514,753
duplication rate = 46.32%
>>>>>>> Insert size
mean insert size = 31,097.5973
std insert size = 1,789,626.5637
median insert size = 217
>>>>>>> Mapping quality
mean mapping quality = 15.1044
>>>>>>> ACTG content
number of A's = 20,457,631 bp (30.28%)
number of C's = 13,901,684 bp (20.58%)
number of T's = 18,819,542 bp (27.86%)
number of G's = 14,382,296 bp (21.29%)
number of N's = 676 bp (0%)
GC percentage = 41.86%
>>>>>>> Mismatches and indels
general error rate = 0.0187
number of mismatches = 1,206,113
number of insertions = 28,282
mapped reads with insertion percentage = 5.66%
number of deletions = 57,198
mapped reads with deletion percentage = 11.3%
homopolymer indels = 47.79%
>>>>>>> Coverage
mean coverageData = 0.0219X
std coverageData = 25.976X
There is a 0.01% of reference with a coverageData >= 1X
There is a 0% 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 1436534 0.005763411919443122 4.761692704306783
chr2 243199373 964722 0.003966794766366441 2.6062564038390312
chr3 198022430 2051555 0.010360215254403251 10.670475360052304
chr4 191154276 78094 4.0853912156273186E-4 0.14382071131925434
chr5 180915260 258656 0.0014297080301573233 0.5185534845343909
chr6 171115067 138771 8.109806017257381E-4 0.45596927780005597
chr7 159138663 2821534 0.017730034592536446 6.642995213443972
chr8 146364022 481998 0.0032931453605449567 1.9458547003457887
chr9 141213431 357745 0.0025333638412907054 1.3669281845918064
chr10 135534747 1213220 0.008951357691323244 4.511192787923484
chr11 135006516 133094 9.858338985653107E-4 0.6482467549758504
chr12 133851895 534108 0.003990290910711424 4.489252958761408
chr13 115169878 125881 0.0010930028075570245 0.7246825902532087
chr14 107349540 19745 1.8393185476155743E-4 0.05485440413264874
chr15 102531392 356501 0.0034769936606341987 2.484211681165303
chr16 90354753 50127 5.547798907712138E-4 0.16241279998751915
chr17 81195210 22080 2.719372238830345E-4 0.0798819607183625
chr18 78077248 49029 6.279550221852081E-4 0.3891776888022461
chr19 59128983 102380 0.0017314689819711597 0.8077374763095614
chr20 63025520 18111 2.8735978695614093E-4 0.10415167284194533
chr21 48129895 98325 0.0020429090900780066 0.6191988029818948
chr22 51304566 25638 4.997216037262648E-4 0.21290450494467272
chrMT 16571 46631918 2814.067829340414 10321.372170251061
chrX 155270560 9838484 0.06336348629128406 30.915227915616143
chrY 59373566 12905 2.1735261782996156E-4 0.11265032207487186