Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 16,819,540
Mapped reads 16,819,540 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 16,819,540 / 100%
Mapped reads, first in pair 8,409,770 / 50%
Mapped reads, second in pair 8,409,770 / 50%
Mapped reads, both in pair 16,819,540 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 91.04
Duplicated reads (estimated) 5,842,633 / 34.74%
Duplication rate 29.29%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 590,301,082 / 38.65%
Number/percentage of C's 174,627,551 / 11.44%
Number/percentage of T's 588,805,638 / 38.56%
Number/percentage of G's 173,370,424 / 11.35%
Number/percentage of N's 83,158 / 0.01%
GC Percentage 22.79%

Coverage

Mean 1.6242
Standard Deviation 8.1547

Mapping Quality

Mean Mapping Quality 24.36

Insert size

Mean 154.54
Standard Deviation 89.54
P25/Median/P75 93 / 130 / 192

Mismatches and indels

General error rate 18.5%
Mismatches 276,886,375
Insertions 1,870,577
Mapped reads with at least one insertion 9.69%
Deletions 1,805,622
Mapped reads with at least one deletion 9.69%
Homopolymer indels 49.58%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 154450475 1.7229 4.9103
PGA_scaffold2__36_contigs__length_69596280 69596280 122551411 1.7609 6.2816
PGA_scaffold3__111_contigs__length_57743597 57743597 97988729 1.697 5.3864
PGA_scaffold4__129_contigs__length_65288255 65288255 104587676 1.6019 7.1667
PGA_scaffold5__109_contigs__length_67248332 67248332 95450741 1.4194 5.3915
PGA_scaffold6__104_contigs__length_61759565 61759565 93473676 1.5135 7.4512
PGA_scaffold7__69_contigs__length_43120122 43120122 69396469 1.6094 5.0041
PGA_scaffold8__63_contigs__length_61151155 61151155 100514192 1.6437 5.5055
PGA_scaffold9__45_contigs__length_38581958 38581958 69178967 1.793 12.0754
PGA_scaffold10__49_contigs__length_53961475 53961475 82680518 1.5322 4.7506
PGA_scaffold11__79_contigs__length_51449921 51449921 71761343 1.3948 5.2663
PGA_scaffold12__71_contigs__length_50438331 50438331 87512788 1.735 6.9194
PGA_scaffold13__52_contigs__length_44396874 44396874 72112296 1.6243 6.0277
PGA_scaffold14__91_contigs__length_45393038 45393038 93318157 2.0558 22.8948
PGA_scaffold15__101_contigs__length_47938513 47938513 64341649 1.3422 5.1697
PGA_scaffold16__33_contigs__length_31980953 31980953 53906293 1.6856 11.9042
PGA_scaffold17__51_contigs__length_34923512 34923512 57505222 1.6466 5.5449
PGA_scaffold18__69_contigs__length_27737463 27737463 39829443 1.4359 7.1276

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 13:20:34
    Generated by QualiMap v.2.2.1