Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 18,940,212
Mapped reads 18,940,212 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 18,940,212 / 100%
Mapped reads, first in pair 9,470,106 / 50%
Mapped reads, second in pair 9,470,106 / 50%
Mapped reads, both in pair 18,940,212 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 92.55
Duplicated reads (estimated) 6,078,879 / 32.1%
Duplication rate 27.2%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 679,724,638 / 38.87%
Number/percentage of C's 195,535,223 / 11.18%
Number/percentage of T's 678,451,117 / 38.8%
Number/percentage of G's 194,815,246 / 11.14%
Number/percentage of N's 22,998 / 0%
GC Percentage 22.32%

Coverage

Mean 1.8595
Standard Deviation 7.5851

Mapping Quality

Mean Mapping Quality 25.03

Insert size

Mean 165.8
Standard Deviation 91.4
P25/Median/P75 101 / 143 / 209

Mismatches and indels

General error rate 18.69%
Mismatches 321,079,339
Insertions 1,956,531
Mapped reads with at least one insertion 9.03%
Deletions 2,001,663
Mapped reads with at least one deletion 9.56%
Homopolymer indels 51.87%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 177312438 1.978 4.7169
PGA_scaffold2__36_contigs__length_69596280 69596280 140341469 2.0165 5.9844
PGA_scaffold3__111_contigs__length_57743597 57743597 111142150 1.9248 5.4298
PGA_scaffold4__129_contigs__length_65288255 65288255 123580306 1.8928 7.171
PGA_scaffold5__109_contigs__length_67248332 67248332 108927820 1.6198 5.0081
PGA_scaffold6__104_contigs__length_61759565 61759565 107560646 1.7416 6.9283
PGA_scaffold7__69_contigs__length_43120122 43120122 78791702 1.8273 5.1474
PGA_scaffold8__63_contigs__length_61151155 61151155 113821693 1.8613 5.569
PGA_scaffold9__45_contigs__length_38581958 38581958 77977613 2.0211 12.0223
PGA_scaffold10__49_contigs__length_53961475 53961475 93958768 1.7412 4.4093
PGA_scaffold11__79_contigs__length_51449921 51449921 85453281 1.6609 5.6921
PGA_scaffold12__71_contigs__length_50438331 50438331 99426792 1.9713 6.6549
PGA_scaffold13__52_contigs__length_44396874 44396874 81369888 1.8328 5.6638
PGA_scaffold14__91_contigs__length_45393038 45393038 105462823 2.3233 20.6292
PGA_scaffold15__101_contigs__length_47938513 47938513 74519857 1.5545 4.9187
PGA_scaffold16__33_contigs__length_31980953 31980953 61408218 1.9201 8.8732
PGA_scaffold17__51_contigs__length_34923512 34923512 66172956 1.8948 5.1833
PGA_scaffold18__69_contigs__length_27737463 27737463 45052489 1.6242 6.2043

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 13:50:50
    Generated by QualiMap v.2.2.1