Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,661,652
Mapped reads 12,661,652 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,661,652 / 100%
Mapped reads, first in pair 6,330,826 / 50%
Mapped reads, second in pair 6,330,826 / 50%
Mapped reads, both in pair 12,661,652 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 86.92
Duplicated reads (estimated) 4,313,688 / 34.07%
Duplication rate 33.09%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 424,205,058 / 38.65%
Number/percentage of C's 125,835,926 / 11.47%
Number/percentage of T's 422,830,420 / 38.53%
Number/percentage of G's 124,617,883 / 11.35%
Number/percentage of N's 59,205 / 0.01%
GC Percentage 22.82%

Coverage

Mean 1.1672
Standard Deviation 7.2429

Mapping Quality

Mean Mapping Quality 24.02

Insert size

Mean 136.72
Standard Deviation 84.68
P25/Median/P75 78 / 114 / 169

Mismatches and indels

General error rate 18.69%
Mismatches 200,912,026
Insertions 1,402,371
Mapped reads with at least one insertion 9.7%
Deletions 1,305,976
Mapped reads with at least one deletion 9.34%
Homopolymer indels 48.78%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 110149095 1.2287 3.8296
PGA_scaffold2__36_contigs__length_69596280 69596280 88679250 1.2742 5.5621
PGA_scaffold3__111_contigs__length_57743597 57743597 69909182 1.2107 4.0207
PGA_scaffold4__129_contigs__length_65288255 65288255 76580536 1.173 5.9913
PGA_scaffold5__109_contigs__length_67248332 67248332 68143965 1.0133 4.1109
PGA_scaffold6__104_contigs__length_61759565 61759565 68234221 1.1048 6.7409
PGA_scaffold7__69_contigs__length_43120122 43120122 49403185 1.1457 3.6141
PGA_scaffold8__63_contigs__length_61151155 61151155 71370358 1.1671 4.065
PGA_scaffold9__45_contigs__length_38581958 38581958 50267396 1.3029 10.328
PGA_scaffold10__49_contigs__length_53961475 53961475 58219592 1.0789 3.3783
PGA_scaffold11__79_contigs__length_51449921 51449921 53024427 1.0306 4.3735
PGA_scaffold12__71_contigs__length_50438331 50438331 62299262 1.2352 5.1275
PGA_scaffold13__52_contigs__length_44396874 44396874 51140211 1.1519 4.5472
PGA_scaffold14__91_contigs__length_45393038 45393038 66651759 1.4683 20.8424
PGA_scaffold15__101_contigs__length_47938513 47938513 46064589 0.9609 3.7644
PGA_scaffold16__33_contigs__length_31980953 31980953 40352004 1.2618 14.8933
PGA_scaffold17__51_contigs__length_34923512 34923512 40982793 1.1735 4.557
PGA_scaffold18__69_contigs__length_27737463 27737463 28471567 1.0265 5.9599

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 13:28:57
    Generated by QualiMap v.2.2.1