Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 8,388,516
Mapped reads 8,388,516 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 8,388,516 / 100%
Mapped reads, first in pair 4,194,258 / 50%
Mapped reads, second in pair 4,194,258 / 50%
Mapped reads, both in pair 8,388,516 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 92.97
Duplicated reads (estimated) 2,373,346 / 28.29%
Duplication rate 22.94%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 292,657,344 / 37.95%
Number/percentage of C's 94,309,293 / 12.23%
Number/percentage of T's 291,335,749 / 37.78%
Number/percentage of G's 92,762,671 / 12.03%
Number/percentage of N's 48,412 / 0.01%
GC Percentage 24.26%

Coverage

Mean 0.8226
Standard Deviation 7.1407

Mapping Quality

Mean Mapping Quality 19.64

Insert size

Mean 167.3
Standard Deviation 94.11
P25/Median/P75 101 / 137 / 206

Mismatches and indels

General error rate 21.2%
Mismatches 153,183,192
Insertions 3,224,390
Mapped reads with at least one insertion 22.19%
Deletions 1,951,452
Mapped reads with at least one deletion 17.6%
Homopolymer indels 39.35%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 74664821 0.8329 3.694
PGA_scaffold2__36_contigs__length_69596280 69596280 60306670 0.8665 4.4456
PGA_scaffold3__111_contigs__length_57743597 57743597 48393443 0.8381 3.7493
PGA_scaffold4__129_contigs__length_65288255 65288255 52915919 0.8105 8.4715
PGA_scaffold5__109_contigs__length_67248332 67248332 49286780 0.7329 4.4074
PGA_scaffold6__104_contigs__length_61759565 61759565 47737952 0.773 5.869
PGA_scaffold7__69_contigs__length_43120122 43120122 34707417 0.8049 3.5123
PGA_scaffold8__63_contigs__length_61151155 61151155 49638539 0.8117 3.7619
PGA_scaffold9__45_contigs__length_38581958 38581958 36881659 0.9559 11.4117
PGA_scaffold10__49_contigs__length_53961475 53961475 41352382 0.7663 4.2361
PGA_scaffold11__79_contigs__length_51449921 51449921 37032811 0.7198 4.176
PGA_scaffold12__71_contigs__length_50438331 50438331 43883503 0.87 5.4282
PGA_scaffold13__52_contigs__length_44396874 44396874 36231303 0.8161 4.3951
PGA_scaffold14__91_contigs__length_45393038 45393038 48540667 1.0693 19.8348
PGA_scaffold15__101_contigs__length_47938513 47938513 32620375 0.6805 3.4162
PGA_scaffold16__33_contigs__length_31980953 31980953 29275423 0.9154 12.9596
PGA_scaffold17__51_contigs__length_34923512 34923512 30056320 0.8606 5.0125
PGA_scaffold18__69_contigs__length_27737463 27737463 21630851 0.7798 6.6224

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
    • 2019/08/12 17:01:32
    Generated by QualiMap v.2.2.1