Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 9,823,244
Mapped reads 9,823,244 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 9,823,244 / 100%
Mapped reads, first in pair 4,911,622 / 50%
Mapped reads, second in pair 4,911,622 / 50%
Mapped reads, both in pair 9,823,244 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 84.11
Duplicated reads (estimated) 3,394,298 / 34.55%
Duplication rate 34.32%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 315,615,238 / 38.31%
Number/percentage of C's 97,235,272 / 11.8%
Number/percentage of T's 314,735,869 / 38.2%
Number/percentage of G's 96,340,194 / 11.69%
Number/percentage of N's 47,686 / 0.01%
GC Percentage 23.49%

Coverage

Mean 0.8763
Standard Deviation 6.0043

Mapping Quality

Mean Mapping Quality 24.21

Insert size

Mean 139.14
Standard Deviation 94.15
P25/Median/P75 70 / 113 / 178

Mismatches and indels

General error rate 18.71%
Mismatches 151,022,684
Insertions 1,049,248
Mapped reads with at least one insertion 9.36%
Deletions 975,581
Mapped reads with at least one deletion 8.99%
Homopolymer indels 49.02%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 83444154 0.9308 2.9944
PGA_scaffold2__36_contigs__length_69596280 69596280 65892338 0.9468 4.3847
PGA_scaffold3__111_contigs__length_57743597 57743597 52599476 0.9109 3.1701
PGA_scaffold4__129_contigs__length_65288255 65288255 56245205 0.8615 4.5432
PGA_scaffold5__109_contigs__length_67248332 67248332 51371126 0.7639 3.3749
PGA_scaffold6__104_contigs__length_61759565 61759565 50642314 0.82 5.372
PGA_scaffold7__69_contigs__length_43120122 43120122 36849758 0.8546 2.9765
PGA_scaffold8__63_contigs__length_61151155 61151155 53865828 0.8809 3.5018
PGA_scaffold9__45_contigs__length_38581958 38581958 37445402 0.9705 8.8095
PGA_scaffold10__49_contigs__length_53961475 53961475 44235294 0.8198 2.6886
PGA_scaffold11__79_contigs__length_51449921 51449921 39249561 0.7629 3.7318
PGA_scaffold12__71_contigs__length_50438331 50438331 47189554 0.9356 4.3309
PGA_scaffold13__52_contigs__length_44396874 44396874 38527219 0.8678 3.6068
PGA_scaffold14__91_contigs__length_45393038 45393038 51348414 1.1312 18.0771
PGA_scaffold15__101_contigs__length_47938513 47938513 34237901 0.7142 2.9345
PGA_scaffold16__33_contigs__length_31980953 31980953 30243227 0.9457 11.5118
PGA_scaffold17__51_contigs__length_34923512 34923512 30793575 0.8817 3.427
PGA_scaffold18__69_contigs__length_27737463 27737463 21574253 0.7778 5.0117

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 13:11:53
    Generated by QualiMap v.2.2.1