Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,841,222
Mapped reads 12,841,222 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,841,222 / 100%
Mapped reads, first in pair 6,420,611 / 50%
Mapped reads, second in pair 6,420,611 / 50%
Mapped reads, both in pair 12,841,222 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 85.22
Duplicated reads (estimated) 4,619,682 / 35.98%
Duplication rate 34.67%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 419,039,444 / 38.4%
Number/percentage of C's 127,759,759 / 11.71%
Number/percentage of T's 417,753,360 / 38.28%
Number/percentage of G's 126,759,997 / 11.62%
Number/percentage of N's 77,717 / 0.01%
GC Percentage 23.32%

Coverage

Mean 1.1606
Standard Deviation 6.1383

Mapping Quality

Mean Mapping Quality 24.13

Insert size

Mean 141.08
Standard Deviation 92.52
P25/Median/P75 73 / 116 / 181

Mismatches and indels

General error rate 18.6%
Mismatches 199,162,373
Insertions 1,333,685
Mapped reads with at least one insertion 9.07%
Deletions 1,261,677
Mapped reads with at least one deletion 8.88%
Homopolymer indels 49.36%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 110923737 1.2374 3.5819
PGA_scaffold2__36_contigs__length_69596280 69596280 88078763 1.2656 4.7851
PGA_scaffold3__111_contigs__length_57743597 57743597 70214937 1.216 3.9585
PGA_scaffold4__129_contigs__length_65288255 65288255 75718880 1.1598 5.1672
PGA_scaffold5__109_contigs__length_67248332 67248332 67763682 1.0077 3.7582
PGA_scaffold6__104_contigs__length_61759565 61759565 66467357 1.0762 5.1128
PGA_scaffold7__69_contigs__length_43120122 43120122 49133874 1.1395 3.6831
PGA_scaffold8__63_contigs__length_61151155 61151155 71407683 1.1677 4.0529
PGA_scaffold9__45_contigs__length_38581958 38581958 49236385 1.2762 8.9142
PGA_scaffold10__49_contigs__length_53961475 53961475 58763839 1.089 3.4535
PGA_scaffold11__79_contigs__length_51449921 51449921 52502550 1.0205 4.2709
PGA_scaffold12__71_contigs__length_50438331 50438331 62086635 1.2309 4.9785
PGA_scaffold13__52_contigs__length_44396874 44396874 51164360 1.1524 4.0953
PGA_scaffold14__91_contigs__length_45393038 45393038 66848634 1.4727 17.7307
PGA_scaffold15__101_contigs__length_47938513 47938513 45300185 0.945 3.6689
PGA_scaffold16__33_contigs__length_31980953 31980953 38773954 1.2124 9.662
PGA_scaffold17__51_contigs__length_34923512 34923512 41141867 1.1781 4.0234
PGA_scaffold18__69_contigs__length_27737463 27737463 28191568 1.0164 5.5017

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 14:08:43
    Generated by QualiMap v.2.2.1