Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 17,891,018
Mapped reads 17,891,018 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 17,891,018 / 100%
Mapped reads, first in pair 8,945,509 / 50%
Mapped reads, second in pair 8,945,509 / 50%
Mapped reads, both in pair 17,891,018 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 87.21
Duplicated reads (estimated) 6,811,589 / 38.07%
Duplication rate 33.99%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 597,891,806 / 38.42%
Number/percentage of C's 181,787,529 / 11.68%
Number/percentage of T's 596,143,346 / 38.31%
Number/percentage of G's 180,211,645 / 11.58%
Number/percentage of N's 91,358 / 0.01%
GC Percentage 23.26%

Coverage

Mean 1.6549
Standard Deviation 9.8777

Mapping Quality

Mean Mapping Quality 24.41

Insert size

Mean 143.46
Standard Deviation 90.47
P25/Median/P75 80 / 119 / 180

Mismatches and indels

General error rate 18.54%
Mismatches 282,693,427
Insertions 1,912,017
Mapped reads with at least one insertion 9.33%
Deletions 1,828,229
Mapped reads with at least one deletion 9.24%
Homopolymer indels 49.64%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 158546193 1.7686 5.5985
PGA_scaffold2__36_contigs__length_69596280 69596280 125767694 1.8071 7.4277
PGA_scaffold3__111_contigs__length_57743597 57743597 99553658 1.7241 5.4844
PGA_scaffold4__129_contigs__length_65288255 65288255 105736931 1.6195 7.8473
PGA_scaffold5__109_contigs__length_67248332 67248332 96586650 1.4363 5.7088
PGA_scaffold6__104_contigs__length_61759565 61759565 95502558 1.5464 10.1086
PGA_scaffold7__69_contigs__length_43120122 43120122 69693650 1.6163 5.0366
PGA_scaffold8__63_contigs__length_61151155 61151155 101695159 1.663 5.7376
PGA_scaffold9__45_contigs__length_38581958 38581958 70936155 1.8386 14.2083
PGA_scaffold10__49_contigs__length_53961475 53961475 84313143 1.5625 4.7521
PGA_scaffold11__79_contigs__length_51449921 51449921 74163723 1.4415 6.2564
PGA_scaffold12__71_contigs__length_50438331 50438331 88389622 1.7524 6.8537
PGA_scaffold13__52_contigs__length_44396874 44396874 73294725 1.6509 6.2459
PGA_scaffold14__91_contigs__length_45393038 45393038 95233626 2.098 26.4597
PGA_scaffold15__101_contigs__length_47938513 47938513 64606599 1.3477 5.2421
PGA_scaffold16__33_contigs__length_31980953 31980953 56313646 1.7608 22.3397
PGA_scaffold17__51_contigs__length_34923512 34923512 58263635 1.6683 6.618
PGA_scaffold18__69_contigs__length_27737463 27737463 40905329 1.4747 8.8894

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 13:06:45
    Generated by QualiMap v.2.2.1