Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 17,152,034
Mapped reads 17,152,034 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 17,152,034 / 100%
Mapped reads, first in pair 8,576,017 / 50%
Mapped reads, second in pair 8,576,017 / 50%
Mapped reads, both in pair 17,152,034 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 85.19
Duplicated reads (estimated) 6,912,255 / 40.3%
Duplication rate 36.66%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 556,883,612 / 38.21%
Number/percentage of C's 172,807,661 / 11.86%
Number/percentage of T's 555,694,134 / 38.13%
Number/percentage of G's 171,980,716 / 11.8%
Number/percentage of N's 103,761 / 0.01%
GC Percentage 23.66%

Coverage

Mean 1.5499
Standard Deviation 6.8682

Mapping Quality

Mean Mapping Quality 24.23

Insert size

Mean 139.03
Standard Deviation 90.24
P25/Median/P75 74 / 116 / 177

Mismatches and indels

General error rate 18.39%
Mismatches 262,798,642
Insertions 1,725,123
Mapped reads with at least one insertion 8.8%
Deletions 1,654,467
Mapped reads with at least one deletion 8.73%
Homopolymer indels 49.02%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 148334339 1.6547 4.8625
PGA_scaffold2__36_contigs__length_69596280 69596280 117317183 1.6857 5.7882
PGA_scaffold3__111_contigs__length_57743597 57743597 93866358 1.6256 5.4953
PGA_scaffold4__129_contigs__length_65288255 65288255 99768975 1.5281 6.2392
PGA_scaffold5__109_contigs__length_67248332 67248332 91025154 1.3536 5.0151
PGA_scaffold6__104_contigs__length_61759565 61759565 88749564 1.437 6.354
PGA_scaffold7__69_contigs__length_43120122 43120122 65885782 1.528 4.9073
PGA_scaffold8__63_contigs__length_61151155 61151155 96292386 1.5747 5.5483
PGA_scaffold9__45_contigs__length_38581958 38581958 65416209 1.6955 10.1087
PGA_scaffold10__49_contigs__length_53961475 53961475 78947286 1.463 4.5809
PGA_scaffold11__79_contigs__length_51449921 51449921 70125807 1.363 5.514
PGA_scaffold12__71_contigs__length_50438331 50438331 83433409 1.6542 6.3576
PGA_scaffold13__52_contigs__length_44396874 44396874 68442824 1.5416 5.7212
PGA_scaffold14__91_contigs__length_45393038 45393038 88154175 1.942 16.3117
PGA_scaffold15__101_contigs__length_47938513 47938513 60829679 1.2689 4.963
PGA_scaffold16__33_contigs__length_31980953 31980953 50944821 1.593 9.231
PGA_scaffold17__51_contigs__length_34923512 34923512 54724207 1.567 5.5021
PGA_scaffold18__69_contigs__length_27737463 27737463 38285751 1.3803 7.1496

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 14:07:14
    Generated by QualiMap v.2.2.1