Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 20,579,756
Mapped reads 20,579,756 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 20,579,756 / 100%
Mapped reads, first in pair 10,289,878 / 50%
Mapped reads, second in pair 10,289,878 / 50%
Mapped reads, both in pair 20,579,756 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 89.76
Duplicated reads (estimated) 7,373,974 / 35.83%
Duplication rate 31.63%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 714,385,066 / 38.77%
Number/percentage of C's 208,419,486 / 11.31%
Number/percentage of T's 712,784,315 / 38.68%
Number/percentage of G's 207,103,369 / 11.24%
Number/percentage of N's 24,986 / 0%
GC Percentage 22.55%

Coverage

Mean 1.9595
Standard Deviation 8.3779

Mapping Quality

Mean Mapping Quality 24.86

Insert size

Mean 153.08
Standard Deviation 90.34
P25/Median/P75 88 / 130 / 194

Mismatches and indels

General error rate 18.78%
Mismatches 339,982,893
Insertions 2,087,864
Mapped reads with at least one insertion 8.88%
Deletions 2,065,955
Mapped reads with at least one deletion 9.1%
Homopolymer indels 51.06%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 186140410 2.0764 5.2036
PGA_scaffold2__36_contigs__length_69596280 69596280 147907888 2.1252 6.5677
PGA_scaffold3__111_contigs__length_57743597 57743597 118041875 2.0442 5.837
PGA_scaffold4__129_contigs__length_65288255 65288255 128333535 1.9656 7.7264
PGA_scaffold5__109_contigs__length_67248332 67248332 114525959 1.703 5.7728
PGA_scaffold6__104_contigs__length_61759565 61759565 114150574 1.8483 7.8284
PGA_scaffold7__69_contigs__length_43120122 43120122 82792397 1.92 5.41
PGA_scaffold8__63_contigs__length_61151155 61151155 120507458 1.9706 6.6611
PGA_scaffold9__45_contigs__length_38581958 38581958 82429463 2.1365 13.1165
PGA_scaffold10__49_contigs__length_53961475 53961475 98519079 1.8257 4.8088
PGA_scaffold11__79_contigs__length_51449921 51449921 90836684 1.7655 6.521
PGA_scaffold12__71_contigs__length_50438331 50438331 104330743 2.0685 7.179
PGA_scaffold13__52_contigs__length_44396874 44396874 85285248 1.921 6.1301
PGA_scaffold14__91_contigs__length_45393038 45393038 112135218 2.4703 22.763
PGA_scaffold15__101_contigs__length_47938513 47938513 78107599 1.6293 5.4649
PGA_scaffold16__33_contigs__length_31980953 31980953 65066050 2.0345 9.7714
PGA_scaffold17__51_contigs__length_34923512 34923512 69615968 1.9934 5.6774
PGA_scaffold18__69_contigs__length_27737463 27737463 47836976 1.7246 6.9575

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 13:59:56
    Generated by QualiMap v.2.2.1