Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 20,265,794
Mapped reads 20,265,794 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 20,265,794 / 100%
Mapped reads, first in pair 10,132,897 / 50%
Mapped reads, second in pair 10,132,897 / 50%
Mapped reads, both in pair 20,265,794 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 92
Duplicated reads (estimated) 6,726,344 / 33.19%
Duplication rate 26.97%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 706,864,967 / 38.31%
Number/percentage of C's 217,642,324 / 11.8%
Number/percentage of T's 704,629,480 / 38.19%
Number/percentage of G's 215,871,703 / 11.7%
Number/percentage of N's 118,292 / 0.01%
GC Percentage 23.5%

Coverage

Mean 1.9679
Standard Deviation 12.3104

Mapping Quality

Mean Mapping Quality 20.37

Insert size

Mean 163.68
Standard Deviation 92.94
P25/Median/P75 98 / 134 / 201

Mismatches and indels

General error rate 20.98%
Mismatches 364,698,818
Insertions 6,986,308
Mapped reads with at least one insertion 20.56%
Deletions 4,395,437
Mapped reads with at least one deletion 16.76%
Homopolymer indels 41.32%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 182203632 2.0325 6.5568
PGA_scaffold2__36_contigs__length_69596280 69596280 145591381 2.0919 8.9685
PGA_scaffold3__111_contigs__length_57743597 57743597 116373590 2.0154 7.0527
PGA_scaffold4__129_contigs__length_65288255 65288255 127624568 1.9548 14.9751
PGA_scaffold5__109_contigs__length_67248332 67248332 118566986 1.7631 8.6247
PGA_scaffold6__104_contigs__length_61759565 61759565 115084490 1.8634 9.6946
PGA_scaffold7__69_contigs__length_43120122 43120122 82297733 1.9086 6.4329
PGA_scaffold8__63_contigs__length_61151155 61151155 119594411 1.9557 7.0644
PGA_scaffold9__45_contigs__length_38581958 38581958 86253260 2.2356 21.7843
PGA_scaffold10__49_contigs__length_53961475 53961475 98520656 1.8258 6.5753
PGA_scaffold11__79_contigs__length_51449921 51449921 89589318 1.7413 7.7523
PGA_scaffold12__71_contigs__length_50438331 50438331 103945633 2.0608 9.1878
PGA_scaffold13__52_contigs__length_44396874 44396874 85974094 1.9365 8.5446
PGA_scaffold14__91_contigs__length_45393038 45393038 113334050 2.4967 30.1134
PGA_scaffold15__101_contigs__length_47938513 47938513 78895161 1.6458 6.447
PGA_scaffold16__33_contigs__length_31980953 31980953 69567532 2.1753 24.3066
PGA_scaffold17__51_contigs__length_34923512 34923512 69876705 2.0008 7.808
PGA_scaffold18__69_contigs__length_27737463 27737463 51125809 1.8432 13.0972

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
    • 2019/08/12 16:58:47
    Generated by QualiMap v.2.2.1