Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 15,671,672
Mapped reads 15,671,672 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 15,671,672 / 100%
Mapped reads, first in pair 7,835,836 / 50%
Mapped reads, second in pair 7,835,836 / 50%
Mapped reads, both in pair 15,671,672 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 93.54
Duplicated reads (estimated) 4,533,872 / 28.93%
Duplication rate 24.4%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 567,981,952 / 38.84%
Number/percentage of C's 164,384,034 / 11.24%
Number/percentage of T's 566,574,626 / 38.75%
Number/percentage of G's 163,266,399 / 11.17%
Number/percentage of N's 19,125 / 0%
GC Percentage 22.41%

Coverage

Mean 1.555
Standard Deviation 8.0501

Mapping Quality

Mean Mapping Quality 24.53

Insert size

Mean 166.06
Standard Deviation 88.52
P25/Median/P75 104 / 144 / 207

Mismatches and indels

General error rate 18.92%
Mismatches 271,630,273
Insertions 1,671,547
Mapped reads with at least one insertion 9.31%
Deletions 1,698,059
Mapped reads with at least one deletion 9.8%
Homopolymer indels 51.42%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 148172792 1.6529 4.3532
PGA_scaffold2__36_contigs__length_69596280 69596280 117195488 1.6839 6.1736
PGA_scaffold3__111_contigs__length_57743597 57743597 93650388 1.6218 4.8408
PGA_scaffold4__129_contigs__length_65288255 65288255 102605659 1.5716 7.1181
PGA_scaffold5__109_contigs__length_67248332 67248332 91615846 1.3624 5.0125
PGA_scaffold6__104_contigs__length_61759565 61759565 90101738 1.4589 6.6238
PGA_scaffold7__69_contigs__length_43120122 43120122 65251675 1.5133 4.5019
PGA_scaffold8__63_contigs__length_61151155 61151155 95584669 1.5631 5.4947
PGA_scaffold9__45_contigs__length_38581958 38581958 66150998 1.7146 13.0418
PGA_scaffold10__49_contigs__length_53961475 53961475 77182693 1.4303 3.8726
PGA_scaffold11__79_contigs__length_51449921 51449921 71505968 1.3898 5.4802
PGA_scaffold12__71_contigs__length_50438331 50438331 82979589 1.6452 6.1166
PGA_scaffold13__52_contigs__length_44396874 44396874 66952845 1.5081 5.1013
PGA_scaffold14__91_contigs__length_45393038 45393038 89507425 1.9718 23.9063
PGA_scaffold15__101_contigs__length_47938513 47938513 62098291 1.2954 4.5731
PGA_scaffold16__33_contigs__length_31980953 31980953 52144119 1.6305 11.0145
PGA_scaffold17__51_contigs__length_34923512 34923512 54339674 1.556 4.6953
PGA_scaffold18__69_contigs__length_27737463 27737463 38335373 1.3821 7.0043

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 13:38:49
    Generated by QualiMap v.2.2.1