Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,984,772
Mapped reads 12,984,772 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,984,772 / 100%
Mapped reads, first in pair 6,492,386 / 50%
Mapped reads, second in pair 6,492,386 / 50%
Mapped reads, both in pair 12,984,772 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 90.88
Duplicated reads (estimated) 4,283,279 / 32.99%
Duplication rate 28.39%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 453,623,227 / 38.55%
Number/percentage of C's 136,261,091 / 11.58%
Number/percentage of T's 452,115,445 / 38.42%
Number/percentage of G's 134,746,867 / 11.45%
Number/percentage of N's 64,475 / 0.01%
GC Percentage 23.03%

Coverage

Mean 1.2516
Standard Deviation 8.9775

Mapping Quality

Mean Mapping Quality 23.65

Insert size

Mean 151.25
Standard Deviation 87.86
P25/Median/P75 91 / 127 / 186

Mismatches and indels

General error rate 18.82%
Mismatches 216,839,513
Insertions 1,469,290
Mapped reads with at least one insertion 9.84%
Deletions 1,402,829
Mapped reads with at least one deletion 9.75%
Homopolymer indels 48.68%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 117504144 1.3108 4.7488
PGA_scaffold2__36_contigs__length_69596280 69596280 94523766 1.3582 6.9248
PGA_scaffold3__111_contigs__length_57743597 57743597 75077322 1.3002 4.7328
PGA_scaffold4__129_contigs__length_65288255 65288255 80598673 1.2345 6.8725
PGA_scaffold5__109_contigs__length_67248332 67248332 73165153 1.088 4.8924
PGA_scaffold6__104_contigs__length_61759565 61759565 73198199 1.1852 8.8432
PGA_scaffold7__69_contigs__length_43120122 43120122 52966068 1.2283 4.4356
PGA_scaffold8__63_contigs__length_61151155 61151155 76517797 1.2513 4.7129
PGA_scaffold9__45_contigs__length_38581958 38581958 54353937 1.4088 12.3723
PGA_scaffold10__49_contigs__length_53961475 53961475 62470300 1.1577 3.9196
PGA_scaffold11__79_contigs__length_51449921 51449921 55593706 1.0805 5.32
PGA_scaffold12__71_contigs__length_50438331 50438331 66462994 1.3177 6.1062
PGA_scaffold13__52_contigs__length_44396874 44396874 54909335 1.2368 5.3425
PGA_scaffold14__91_contigs__length_45393038 45393038 73094964 1.6103 24.2024
PGA_scaffold15__101_contigs__length_47938513 47938513 49629133 1.0353 4.5172
PGA_scaffold16__33_contigs__length_31980953 31980953 43431691 1.358 22.046
PGA_scaffold17__51_contigs__length_34923512 34923512 44362830 1.2703 5.7209
PGA_scaffold18__69_contigs__length_27737463 27737463 31547593 1.1374 8.4046

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 13:33:33
    Generated by QualiMap v.2.2.1