Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 8,724,714
Mapped reads 8,724,714 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 8,724,714 / 100%
Mapped reads, first in pair 4,362,357 / 50%
Mapped reads, second in pair 4,362,357 / 50%
Mapped reads, both in pair 8,724,714 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 87.25
Duplicated reads (estimated) 2,846,855 / 32.63%
Duplication rate 31.22%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 291,363,990 / 38.39%
Number/percentage of C's 89,126,197 / 11.74%
Number/percentage of T's 290,405,697 / 38.26%
Number/percentage of G's 88,091,654 / 11.61%
Number/percentage of N's 44,759 / 0.01%
GC Percentage 23.35%

Coverage

Mean 0.8073
Standard Deviation 5.9892

Mapping Quality

Mean Mapping Quality 23.84

Insert size

Mean 145.12
Standard Deviation 92.33
P25/Median/P75 79 / 119 / 183

Mismatches and indels

General error rate 18.78%
Mismatches 139,561,065
Insertions 992,359
Mapped reads with at least one insertion 9.93%
Deletions 918,369
Mapped reads with at least one deletion 9.51%
Homopolymer indels 48.82%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 76418536 0.8525 3.0101
PGA_scaffold2__36_contigs__length_69596280 69596280 61054930 0.8773 4.1254
PGA_scaffold3__111_contigs__length_57743597 57743597 48464744 0.8393 3.0655
PGA_scaffold4__129_contigs__length_65288255 65288255 51833052 0.7939 4.6344
PGA_scaffold5__109_contigs__length_67248332 67248332 47185233 0.7017 3.2175
PGA_scaffold6__104_contigs__length_61759565 61759565 47082271 0.7623 5.6795
PGA_scaffold7__69_contigs__length_43120122 43120122 33932384 0.7869 2.9074
PGA_scaffold8__63_contigs__length_61151155 61151155 49198685 0.8045 3.2467
PGA_scaffold9__45_contigs__length_38581958 38581958 35066239 0.9089 8.678
PGA_scaffold10__49_contigs__length_53961475 53961475 40562905 0.7517 2.5393
PGA_scaffold11__79_contigs__length_51449921 51449921 36125731 0.7022 3.464
PGA_scaffold12__71_contigs__length_50438331 50438331 43487937 0.8622 4.2434
PGA_scaffold13__52_contigs__length_44396874 44396874 35458918 0.7987 3.4009
PGA_scaffold14__91_contigs__length_45393038 45393038 47249997 1.0409 18.2066
PGA_scaffold15__101_contigs__length_47938513 47938513 31385539 0.6547 2.8765
PGA_scaffold16__33_contigs__length_31980953 31980953 27940426 0.8737 11.7821
PGA_scaffold17__51_contigs__length_34923512 34923512 28289819 0.8101 3.4919
PGA_scaffold18__69_contigs__length_27737463 27737463 19982450 0.7204 4.4754

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 13:10:51
    Generated by QualiMap v.2.2.1