Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 18,001,892
Mapped reads 18,001,892 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 18,001,892 / 100%
Mapped reads, first in pair 9,000,946 / 50%
Mapped reads, second in pair 9,000,946 / 50%
Mapped reads, both in pair 18,001,892 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 91.83
Duplicated reads (estimated) 6,162,142 / 34.23%
Duplication rate 28.14%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 635,208,746 / 38.53%
Number/percentage of C's 191,028,549 / 11.59%
Number/percentage of T's 633,213,537 / 38.41%
Number/percentage of G's 189,098,178 / 11.47%
Number/percentage of N's 151,097 / 0.01%
GC Percentage 23.06%

Coverage

Mean 1.7534
Standard Deviation 9.344

Mapping Quality

Mean Mapping Quality 24.43

Insert size

Mean 164.87
Standard Deviation 95.48
P25/Median/P75 97 / 139 / 209

Mismatches and indels

General error rate 18.61%
Mismatches 300,878,189
Insertions 1,971,139
Mapped reads with at least one insertion 9.53%
Deletions 1,930,225
Mapped reads with at least one deletion 9.68%
Homopolymer indels 50.11%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 168568105 1.8804 5.3619
PGA_scaffold2__36_contigs__length_69596280 69596280 133687819 1.9209 7.3441
PGA_scaffold3__111_contigs__length_57743597 57743597 105568776 1.8282 5.792
PGA_scaffold4__129_contigs__length_65288255 65288255 111887540 1.7137 8.1465
PGA_scaffold5__109_contigs__length_67248332 67248332 102442478 1.5233 5.7034
PGA_scaffold6__104_contigs__length_61759565 61759565 101075519 1.6366 7.9753
PGA_scaffold7__69_contigs__length_43120122 43120122 73408585 1.7024 5.2997
PGA_scaffold8__63_contigs__length_61151155 61151155 107817735 1.7631 5.939
PGA_scaffold9__45_contigs__length_38581958 38581958 74885949 1.941 14.2886
PGA_scaffold10__49_contigs__length_53961475 53961475 90309822 1.6736 4.8988
PGA_scaffold11__79_contigs__length_51449921 51449921 78759230 1.5308 6.4614
PGA_scaffold12__71_contigs__length_50438331 50438331 94089988 1.8654 7.3688
PGA_scaffold13__52_contigs__length_44396874 44396874 77509910 1.7458 6.5551
PGA_scaffold14__91_contigs__length_45393038 45393038 100656219 2.2174 26.0585
PGA_scaffold15__101_contigs__length_47938513 47938513 68217120 1.423 5.2942
PGA_scaffold16__33_contigs__length_31980953 31980953 59117990 1.8485 16.2646
PGA_scaffold17__51_contigs__length_34923512 34923512 61178097 1.7518 5.8598
PGA_scaffold18__69_contigs__length_27737463 27737463 43119263 1.5545 9.2436

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 12:57:52
    Generated by QualiMap v.2.2.1