Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 10,300,220
Mapped reads 10,300,220 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 10,300,220 / 100%
Mapped reads, first in pair 5,150,110 / 50%
Mapped reads, second in pair 5,150,110 / 50%
Mapped reads, both in pair 10,300,220 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 87.84
Duplicated reads (estimated) 3,224,299 / 31.3%
Duplication rate 26.91%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 339,910,512 / 37.99%
Number/percentage of C's 108,618,698 / 12.14%
Number/percentage of T's 338,669,066 / 37.85%
Number/percentage of G's 107,624,891 / 12.03%
Number/percentage of N's 56,951 / 0.01%
GC Percentage 24.17%

Coverage

Mean 0.9546
Standard Deviation 7.6143

Mapping Quality

Mean Mapping Quality 19.72

Insert size

Mean 158.19
Standard Deviation 95.11
P25/Median/P75 91 / 126 / 193

Mismatches and indels

General error rate 21%
Mismatches 176,463,156
Insertions 3,630,676
Mapped reads with at least one insertion 21.13%
Deletions 2,231,189
Mapped reads with at least one deletion 16.74%
Homopolymer indels 40.12%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 87381057 0.9748 4.327
PGA_scaffold2__36_contigs__length_69596280 69596280 70175005 1.0083 5.3079
PGA_scaffold3__111_contigs__length_57743597 57743597 55982301 0.9695 3.9345
PGA_scaffold4__129_contigs__length_65288255 65288255 61647153 0.9442 9.3781
PGA_scaffold5__109_contigs__length_67248332 67248332 57142903 0.8497 4.7186
PGA_scaffold6__104_contigs__length_61759565 61759565 55874902 0.9047 7.0552
PGA_scaffold7__69_contigs__length_43120122 43120122 40061368 0.9291 3.5922
PGA_scaffold8__63_contigs__length_61151155 61151155 57651141 0.9428 3.8203
PGA_scaffold9__45_contigs__length_38581958 38581958 42269021 1.0956 12.4156
PGA_scaffold10__49_contigs__length_53961475 53961475 47776295 0.8854 3.9138
PGA_scaffold11__79_contigs__length_51449921 51449921 43274250 0.8411 4.5864
PGA_scaffold12__71_contigs__length_50438331 50438331 50203963 0.9954 5.2219
PGA_scaffold13__52_contigs__length_44396874 44396874 41888345 0.9435 4.7465
PGA_scaffold14__91_contigs__length_45393038 45393038 55612621 1.2251 18.4109
PGA_scaffold15__101_contigs__length_47938513 47938513 38273017 0.7984 3.7215
PGA_scaffold16__33_contigs__length_31980953 31980953 34794457 1.088 17.0972
PGA_scaffold17__51_contigs__length_34923512 34923512 34192767 0.9791 5.0324
PGA_scaffold18__69_contigs__length_27737463 27737463 25345688 0.9138 8.0923

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
    • 2019/08/12 16:52:05
    Generated by QualiMap v.2.2.1