Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 20,933,644
Mapped reads 20,933,644 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 20,933,644 / 100%
Mapped reads, first in pair 10,466,822 / 50%
Mapped reads, second in pair 10,466,822 / 50%
Mapped reads, both in pair 20,933,644 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 91.27
Duplicated reads (estimated) 7,097,969 / 33.91%
Duplication rate 29.51%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 740,834,461 / 38.87%
Number/percentage of C's 213,196,580 / 11.19%
Number/percentage of T's 739,471,449 / 38.8%
Number/percentage of G's 212,359,557 / 11.14%
Number/percentage of N's 25,695 / 0%
GC Percentage 22.33%

Coverage

Mean 2.0268
Standard Deviation 7.952

Mapping Quality

Mean Mapping Quality 25.03

Insert size

Mean 156.55
Standard Deviation 88.45
P25/Median/P75 95 / 134 / 196

Mismatches and indels

General error rate 18.68%
Mismatches 349,710,683
Insertions 2,165,169
Mapped reads with at least one insertion 9.05%
Deletions 2,170,302
Mapped reads with at least one deletion 9.38%
Homopolymer indels 51.39%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 194679434 2.1717 5.1333
PGA_scaffold2__36_contigs__length_69596280 69596280 153602044 2.207 6.3942
PGA_scaffold3__111_contigs__length_57743597 57743597 121866655 2.1105 5.8421
PGA_scaffold4__129_contigs__length_65288255 65288255 133747673 2.0486 7.3313
PGA_scaffold5__109_contigs__length_67248332 67248332 119227350 1.7729 5.3531
PGA_scaffold6__104_contigs__length_61759565 61759565 117492491 1.9024 7.0934
PGA_scaffold7__69_contigs__length_43120122 43120122 85752964 1.9887 5.467
PGA_scaffold8__63_contigs__length_61151155 61151155 124391221 2.0342 5.9635
PGA_scaffold9__45_contigs__length_38581958 38581958 84226478 2.1831 12.23
PGA_scaffold10__49_contigs__length_53961475 53961475 101985805 1.89 4.6902
PGA_scaffold11__79_contigs__length_51449921 51449921 91719013 1.7827 5.7924
PGA_scaffold12__71_contigs__length_50438331 50438331 109028220 2.1616 7.2089
PGA_scaffold13__52_contigs__length_44396874 44396874 88582152 1.9952 6.1265
PGA_scaffold14__91_contigs__length_45393038 45393038 115124433 2.5362 21.5974
PGA_scaffold15__101_contigs__length_47938513 47938513 81056376 1.6908 5.3011
PGA_scaffold16__33_contigs__length_31980953 31980953 66685102 2.0852 9.2017
PGA_scaffold17__51_contigs__length_34923512 34923512 71728706 2.0539 5.4157
PGA_scaffold18__69_contigs__length_27737463 27737463 49028149 1.7676 6.422

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 13:43:52
    Generated by QualiMap v.2.2.1