Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 19,709,486
Mapped reads 19,709,486 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 19,709,486 / 100%
Mapped reads, first in pair 9,854,743 / 50%
Mapped reads, second in pair 9,854,743 / 50%
Mapped reads, both in pair 19,709,486 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 92.25
Duplicated reads (estimated) 6,463,444 / 32.79%
Duplication rate 27.85%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 705,226,236 / 38.88%
Number/percentage of C's 202,951,253 / 11.19%
Number/percentage of T's 703,767,434 / 38.8%
Number/percentage of G's 201,769,724 / 11.12%
Number/percentage of N's 23,624 / 0%
GC Percentage 22.31%

Coverage

Mean 1.9288
Standard Deviation 7.8777

Mapping Quality

Mean Mapping Quality 24.94

Insert size

Mean 162.58
Standard Deviation 89.59
P25/Median/P75 101 / 141 / 204

Mismatches and indels

General error rate 18.7%
Mismatches 333,010,719
Insertions 2,059,794
Mapped reads with at least one insertion 9.13%
Deletions 2,082,395
Mapped reads with at least one deletion 9.56%
Homopolymer indels 51.54%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 184104964 2.0537 5.175
PGA_scaffold2__36_contigs__length_69596280 69596280 145467272 2.0902 6.3286
PGA_scaffold3__111_contigs__length_57743597 57743597 116327019 2.0145 5.6123
PGA_scaffold4__129_contigs__length_65288255 65288255 126593162 1.939 7.1623
PGA_scaffold5__109_contigs__length_67248332 67248332 114397657 1.7011 5.466
PGA_scaffold6__104_contigs__length_61759565 61759565 113512999 1.838 8.8208
PGA_scaffold7__69_contigs__length_43120122 43120122 82454437 1.9122 5.2141
PGA_scaffold8__63_contigs__length_61151155 61151155 118842056 1.9434 6.3442
PGA_scaffold9__45_contigs__length_38581958 38581958 80713905 2.092 12.0664
PGA_scaffold10__49_contigs__length_53961475 53961475 97215133 1.8016 4.6842
PGA_scaffold11__79_contigs__length_51449921 51449921 86981335 1.6906 5.6797
PGA_scaffold12__71_contigs__length_50438331 50438331 103129598 2.0447 7.101
PGA_scaffold13__52_contigs__length_44396874 44396874 83915022 1.8901 5.9636
PGA_scaffold14__91_contigs__length_45393038 45393038 108114870 2.3818 19.9632
PGA_scaffold15__101_contigs__length_47938513 47938513 76797664 1.602 5.2869
PGA_scaffold16__33_contigs__length_31980953 31980953 63264096 1.9782 10.5011
PGA_scaffold17__51_contigs__length_34923512 34923512 68159500 1.9517 5.4052
PGA_scaffold18__69_contigs__length_27737463 27737463 47626221 1.717 6.258

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 13:46:08
    Generated by QualiMap v.2.2.1