Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 15,594,156
Mapped reads 15,594,156 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 15,594,156 / 100%
Mapped reads, first in pair 7,797,078 / 50%
Mapped reads, second in pair 7,797,078 / 50%
Mapped reads, both in pair 15,594,156 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 85.56
Duplicated reads (estimated) 5,739,516 / 36.81%
Duplication rate 35.38%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 512,405,387 / 38.51%
Number/percentage of C's 154,506,628 / 11.61%
Number/percentage of T's 510,769,840 / 38.38%
Number/percentage of G's 152,999,337 / 11.5%
Number/percentage of N's 71,178 / 0.01%
GC Percentage 23.11%

Coverage

Mean 1.4152
Standard Deviation 8.8242

Mapping Quality

Mean Mapping Quality 24.25

Insert size

Mean 135.28
Standard Deviation 86.8
P25/Median/P75 74 / 112 / 169

Mismatches and indels

General error rate 18.75%
Mismatches 244,700,720
Insertions 1,620,602
Mapped reads with at least one insertion 9.11%
Deletions 1,546,918
Mapped reads with at least one deletion 8.99%
Homopolymer indels 49.55%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 132387920 1.4768 5.4774
PGA_scaffold2__36_contigs__length_69596280 69596280 106711114 1.5333 7.076
PGA_scaffold3__111_contigs__length_57743597 57743597 85101351 1.4738 4.8238
PGA_scaffold4__129_contigs__length_65288255 65288255 92389185 1.4151 6.8481
PGA_scaffold5__109_contigs__length_67248332 67248332 83349158 1.2394 5.1165
PGA_scaffold6__104_contigs__length_61759565 61759565 82216032 1.3312 9.7748
PGA_scaffold7__69_contigs__length_43120122 43120122 59984706 1.3911 4.5096
PGA_scaffold8__63_contigs__length_61151155 61151155 86593833 1.4161 5.19
PGA_scaffold9__45_contigs__length_38581958 38581958 60260205 1.5619 12.7597
PGA_scaffold10__49_contigs__length_53961475 53961475 70490682 1.3063 4.1133
PGA_scaffold11__79_contigs__length_51449921 51449921 64535068 1.2543 5.5224
PGA_scaffold12__71_contigs__length_50438331 50438331 74793739 1.4829 6.5972
PGA_scaffold13__52_contigs__length_44396874 44396874 62174665 1.4004 5.6752
PGA_scaffold14__91_contigs__length_45393038 45393038 81422750 1.7937 22.4889
PGA_scaffold15__101_contigs__length_47938513 47938513 56146232 1.1712 4.6591
PGA_scaffold16__33_contigs__length_31980953 31980953 48685520 1.5223 20.2662
PGA_scaffold17__51_contigs__length_34923512 34923512 50569862 1.448 6.0563
PGA_scaffold18__69_contigs__length_27737463 27737463 35774190 1.2897 8.0387

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 13:36:52
    Generated by QualiMap v.2.2.1