Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 14,197,810
Mapped reads 14,197,810 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 14,197,810 / 100%
Mapped reads, first in pair 7,098,905 / 50%
Mapped reads, second in pair 7,098,905 / 50%
Mapped reads, both in pair 14,197,810 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 89.29
Duplicated reads (estimated) 5,023,262 / 35.38%
Duplication rate 30.98%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 484,580,125 / 38.33%
Number/percentage of C's 148,768,734 / 11.77%
Number/percentage of T's 483,258,594 / 38.22%
Number/percentage of G's 147,640,887 / 11.68%
Number/percentage of N's 111,732 / 0.01%
GC Percentage 23.45%

Coverage

Mean 1.3446
Standard Deviation 7.8846

Mapping Quality

Mean Mapping Quality 24.3

Insert size

Mean 152.16
Standard Deviation 92.67
P25/Median/P75 86 / 127 / 192

Mismatches and indels

General error rate 18.54%
Mismatches 229,695,330
Insertions 1,523,412
Mapped reads with at least one insertion 9.36%
Deletions 1,464,216
Mapped reads with at least one deletion 9.32%
Homopolymer indels 49.37%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 131207573 1.4637 4.6107
PGA_scaffold2__36_contigs__length_69596280 69596280 103241024 1.4834 5.9289
PGA_scaffold3__111_contigs__length_57743597 57743597 80117693 1.3875 4.6341
PGA_scaffold4__129_contigs__length_65288255 65288255 84724895 1.2977 6.4094
PGA_scaffold5__109_contigs__length_67248332 67248332 78557783 1.1682 4.797
PGA_scaffold6__104_contigs__length_61759565 61759565 76247709 1.2346 7.4462
PGA_scaffold7__69_contigs__length_43120122 43120122 56616166 1.313 4.3889
PGA_scaffold8__63_contigs__length_61151155 61151155 83087644 1.3587 5.1203
PGA_scaffold9__45_contigs__length_38581958 38581958 57038196 1.4784 11.5025
PGA_scaffold10__49_contigs__length_53961475 53961475 71036558 1.3164 4.1928
PGA_scaffold11__79_contigs__length_51449921 51449921 58473966 1.1365 4.9432
PGA_scaffold12__71_contigs__length_50438331 50438331 73470888 1.4566 6.4835
PGA_scaffold13__52_contigs__length_44396874 44396874 59987573 1.3512 5.4782
PGA_scaffold14__91_contigs__length_45393038 45393038 77334410 1.7037 22.3064
PGA_scaffold15__101_contigs__length_47938513 47938513 51538728 1.0751 4.5346
PGA_scaffold16__33_contigs__length_31980953 31980953 45063236 1.4091 14.1879
PGA_scaffold17__51_contigs__length_34923512 34923512 46172059 1.3221 5.0202
PGA_scaffold18__69_contigs__length_27737463 27737463 33174128 1.196 6.6621

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 12:52:50
    Generated by QualiMap v.2.2.1