Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 5,532,546
Mapped reads 5,532,546 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 5,532,546 / 100%
Mapped reads, first in pair 2,766,273 / 50%
Mapped reads, second in pair 2,766,273 / 50%
Mapped reads, both in pair 5,532,546 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 88.4
Duplicated reads (estimated) 1,596,039 / 28.85%
Duplication rate 28.11%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 186,577,454 / 38.27%
Number/percentage of C's 57,987,758 / 11.89%
Number/percentage of T's 185,804,953 / 38.11%
Number/percentage of G's 57,183,299 / 11.73%
Number/percentage of N's 42,235 / 0.01%
GC Percentage 23.62%

Coverage

Mean 0.5186
Standard Deviation 5.528

Mapping Quality

Mean Mapping Quality 23.1

Insert size

Mean 144.39
Standard Deviation 88.54
P25/Median/P75 83 / 120 / 179

Mismatches and indels

General error rate 18.95%
Mismatches 90,373,225
Insertions 673,942
Mapped reads with at least one insertion 10.63%
Deletions 601,399
Mapped reads with at least one deletion 9.81%
Homopolymer indels 48.02%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 48315005 0.539 2.2571
PGA_scaffold2__36_contigs__length_69596280 69596280 38843079 0.5581 3.7527
PGA_scaffold3__111_contigs__length_57743597 57743597 30514611 0.5285 2.154
PGA_scaffold4__129_contigs__length_65288255 65288255 33287788 0.5099 3.8465
PGA_scaffold5__109_contigs__length_67248332 67248332 30350375 0.4513 2.5882
PGA_scaffold6__104_contigs__length_61759565 61759565 30668130 0.4966 4.9134
PGA_scaffold7__69_contigs__length_43120122 43120122 21708254 0.5034 2.1134
PGA_scaffold8__63_contigs__length_61151155 61151155 31382871 0.5132 2.4347
PGA_scaffold9__45_contigs__length_38581958 38581958 22990171 0.5959 7.5942
PGA_scaffold10__49_contigs__length_53961475 53961475 25675422 0.4758 1.8459
PGA_scaffold11__79_contigs__length_51449921 51449921 23242772 0.4518 2.4878
PGA_scaffold12__71_contigs__length_50438331 50438331 27536344 0.5459 3.1675
PGA_scaffold13__52_contigs__length_44396874 44396874 22661475 0.5104 2.4959
PGA_scaffold14__91_contigs__length_45393038 45393038 31364680 0.691 17.3804
PGA_scaffold15__101_contigs__length_47938513 47938513 20344719 0.4244 2.0211
PGA_scaffold16__33_contigs__length_31980953 31980953 18692213 0.5845 13.126
PGA_scaffold17__51_contigs__length_34923512 34923512 18177855 0.5205 2.7911
PGA_scaffold18__69_contigs__length_27737463 27737463 12935245 0.4663 3.9237

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 12:51:21
    Generated by QualiMap v.2.2.1