Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,766,328
Mapped reads 12,766,328 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,766,328 / 100%
Mapped reads, first in pair 6,383,164 / 50%
Mapped reads, second in pair 6,383,164 / 50%
Mapped reads, both in pair 12,766,328 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 85.61
Duplicated reads (estimated) 4,527,973 / 35.47%
Duplication rate 34.88%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 419,752,058 / 38.51%
Number/percentage of C's 126,549,812 / 11.61%
Number/percentage of T's 418,387,234 / 38.39%
Number/percentage of G's 125,162,279 / 11.48%
Number/percentage of N's 57,799 / 0.01%
GC Percentage 23.1%

Coverage

Mean 1.1591
Standard Deviation 7.9099

Mapping Quality

Mean Mapping Quality 23.93

Insert size

Mean 133.21
Standard Deviation 84.65
P25/Median/P75 74 / 110 / 165

Mismatches and indels

General error rate 18.74%
Mismatches 200,092,350
Insertions 1,378,624
Mapped reads with at least one insertion 9.46%
Deletions 1,292,281
Mapped reads with at least one deletion 9.17%
Homopolymer indels 48.89%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 109136338 1.2174 4.1768
PGA_scaffold2__36_contigs__length_69596280 69596280 87662321 1.2596 6.4324
PGA_scaffold3__111_contigs__length_57743597 57743597 69539983 1.2043 4.2526
PGA_scaffold4__129_contigs__length_65288255 65288255 75646074 1.1586 6.3938
PGA_scaffold5__109_contigs__length_67248332 67248332 67922215 1.01 4.5923
PGA_scaffold6__104_contigs__length_61759565 61759565 66958786 1.0842 6.435
PGA_scaffold7__69_contigs__length_43120122 43120122 49139449 1.1396 3.7281
PGA_scaffold8__63_contigs__length_61151155 61151155 70759284 1.1571 4.5846
PGA_scaffold9__45_contigs__length_38581958 38581958 50287050 1.3034 12.0042
PGA_scaffold10__49_contigs__length_53961475 53961475 57600431 1.0674 3.4456
PGA_scaffold11__79_contigs__length_51449921 51449921 53172451 1.0335 4.8942
PGA_scaffold12__71_contigs__length_50438331 50438331 61890717 1.2271 5.5604
PGA_scaffold13__52_contigs__length_44396874 44396874 50625491 1.1403 4.7286
PGA_scaffold14__91_contigs__length_45393038 45393038 67254854 1.4816 24.3116
PGA_scaffold15__101_contigs__length_47938513 47938513 46053394 0.9607 3.9311
PGA_scaffold16__33_contigs__length_31980953 31980953 39281077 1.2283 12.8946
PGA_scaffold17__51_contigs__length_34923512 34923512 40929983 1.172 4.4464
PGA_scaffold18__69_contigs__length_27737463 27737463 28407965 1.0242 7.0191

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 13:30:24
    Generated by QualiMap v.2.2.1