Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 21,119,008
Mapped reads 21,119,008 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 21,119,008 / 100%
Mapped reads, first in pair 10,559,504 / 50%
Mapped reads, second in pair 10,559,504 / 50%
Mapped reads, both in pair 21,119,008 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 89.3
Duplicated reads (estimated) 7,777,053 / 36.82%
Duplication rate 32.24%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 727,470,103 / 38.67%
Number/percentage of C's 214,288,835 / 11.39%
Number/percentage of T's 726,077,483 / 38.6%
Number/percentage of G's 213,387,730 / 11.34%
Number/percentage of N's 25,543 / 0%
GC Percentage 22.73%

Coverage

Mean 2.0005
Standard Deviation 7.9608

Mapping Quality

Mean Mapping Quality 24.96

Insert size

Mean 152.74
Standard Deviation 90.79
P25/Median/P75 88 / 130 / 194

Mismatches and indels

General error rate 18.59%
Mismatches 343,348,927
Insertions 2,129,514
Mapped reads with at least one insertion 8.84%
Deletions 2,132,145
Mapped reads with at least one deletion 9.15%
Homopolymer indels 51.12%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 191236000 2.1333 5.3417
PGA_scaffold2__36_contigs__length_69596280 69596280 151279456 2.1737 6.245
PGA_scaffold3__111_contigs__length_57743597 57743597 120987771 2.0953 5.956
PGA_scaffold4__129_contigs__length_65288255 65288255 130580464 2.0001 7.1864
PGA_scaffold5__109_contigs__length_67248332 67248332 116281336 1.7291 5.4598
PGA_scaffold6__104_contigs__length_61759565 61759565 115644570 1.8725 8.3896
PGA_scaffold7__69_contigs__length_43120122 43120122 85045926 1.9723 5.5108
PGA_scaffold8__63_contigs__length_61151155 61151155 123847997 2.0253 5.97
PGA_scaffold9__45_contigs__length_38581958 38581958 84316494 2.1854 12.699
PGA_scaffold10__49_contigs__length_53961475 53961475 101794132 1.8864 5.0579
PGA_scaffold11__79_contigs__length_51449921 51449921 91363630 1.7758 6.0357
PGA_scaffold12__71_contigs__length_50438331 50438331 107078106 2.123 7.115
PGA_scaffold13__52_contigs__length_44396874 44396874 87906298 1.98 6.3112
PGA_scaffold14__91_contigs__length_45393038 45393038 113510049 2.5006 20.2897
PGA_scaffold15__101_contigs__length_47938513 47938513 79444917 1.6572 5.4792
PGA_scaffold16__33_contigs__length_31980953 31980953 65774841 2.0567 9.537
PGA_scaffold17__51_contigs__length_34923512 34923512 70788805 2.027 5.8504
PGA_scaffold18__69_contigs__length_27737463 27737463 48331404 1.7425 6.3703

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 13:57:30
    Generated by QualiMap v.2.2.1