Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,785,804
Mapped reads 12,785,804 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,785,804 / 100%
Mapped reads, first in pair 6,392,902 / 50%
Mapped reads, second in pair 6,392,902 / 50%
Mapped reads, both in pair 12,785,804 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 84.8
Duplicated reads (estimated) 4,781,668 / 37.4%
Duplication rate 35.13%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 414,121,407 / 38.3%
Number/percentage of C's 127,735,140 / 11.81%
Number/percentage of T's 412,877,616 / 38.19%
Number/percentage of G's 126,504,300 / 11.7%
Number/percentage of N's 61,448 / 0.01%
GC Percentage 23.51%

Coverage

Mean 1.1499
Standard Deviation 6.7645

Mapping Quality

Mean Mapping Quality 24.44

Insert size

Mean 140.01
Standard Deviation 93.12
P25/Median/P75 73 / 115 / 179

Mismatches and indels

General error rate 18.56%
Mismatches 196,668,652
Insertions 1,325,090
Mapped reads with at least one insertion 9.08%
Deletions 1,256,348
Mapped reads with at least one deletion 8.9%
Homopolymer indels 49.13%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 110189524 1.2292 3.8892
PGA_scaffold2__36_contigs__length_69596280 69596280 87274381 1.254 5.0913
PGA_scaffold3__111_contigs__length_57743597 57743597 69335533 1.2007 4.0137
PGA_scaffold4__129_contigs__length_65288255 65288255 73212908 1.1214 5.3698
PGA_scaffold5__109_contigs__length_67248332 67248332 66999890 0.9963 4.1335
PGA_scaffold6__104_contigs__length_61759565 61759565 65855979 1.0663 6.293
PGA_scaffold7__69_contigs__length_43120122 43120122 48970777 1.1357 3.8398
PGA_scaffold8__63_contigs__length_61151155 61151155 70928376 1.1599 4.2
PGA_scaffold9__45_contigs__length_38581958 38581958 49165940 1.2743 9.7732
PGA_scaffold10__49_contigs__length_53961475 53961475 58841685 1.0904 3.47
PGA_scaffold11__79_contigs__length_51449921 51449921 50844467 0.9882 4.2077
PGA_scaffold12__71_contigs__length_50438331 50438331 61597858 1.2213 5.493
PGA_scaffold13__52_contigs__length_44396874 44396874 50965082 1.1479 4.5859
PGA_scaffold14__91_contigs__length_45393038 45393038 66561509 1.4663 19.4286
PGA_scaffold15__101_contigs__length_47938513 47938513 45146715 0.9418 3.7313
PGA_scaffold16__33_contigs__length_31980953 31980953 38709582 1.2104 12.0368
PGA_scaffold17__51_contigs__length_34923512 34923512 40650300 1.164 4.5011
PGA_scaffold18__69_contigs__length_27737463 27737463 28362530 1.0225 5.9474

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram 

Contents

  • Summary
  • Coverage across reference
  • Coverage Histogram
  • Coverage Histogram (0-50X)
  • Genome Fraction Coverage
  • Duplication Rate Histogram
  • Mapped Reads Nucleotide Content
  • Mapped Reads GC-content Distribution
  • Homopolymer Indels
  • Mapping Quality Across Reference
  • Mapping Quality Histogram
  • Insert Size Across Reference
  • Insert Size Histogram
    • 2019/09/12 13:09:53
    Generated by QualiMap v.2.2.1