Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,385,666
Mapped reads 12,385,666 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,385,666 / 100%
Mapped reads, first in pair 6,192,833 / 50%
Mapped reads, second in pair 6,192,833 / 50%
Mapped reads, both in pair 12,385,666 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 83.2
Duplicated reads (estimated) 4,518,940 / 36.49%
Duplication rate 37%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 395,378,404 / 38.47%
Number/percentage of C's 119,569,487 / 11.63%
Number/percentage of T's 394,219,171 / 38.36%
Number/percentage of G's 118,508,761 / 11.53%
Number/percentage of N's 85,964 / 0.01%
GC Percentage 23.17%

Coverage

Mean 1.0929
Standard Deviation 7.0497

Mapping Quality

Mean Mapping Quality 24.4

Insert size

Mean 130.19
Standard Deviation 87.33
P25/Median/P75 68 / 106 / 164

Mismatches and indels

General error rate 18.65%
Mismatches 187,997,811
Insertions 1,256,965
Mapped reads with at least one insertion 8.9%
Deletions 1,185,481
Mapped reads with at least one deletion 8.69%
Homopolymer indels 49.69%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 104243013 1.1629 3.8957
PGA_scaffold2__36_contigs__length_69596280 69596280 82564157 1.1863 5.342
PGA_scaffold3__111_contigs__length_57743597 57743597 65696196 1.1377 3.6593
PGA_scaffold4__129_contigs__length_65288255 65288255 71244067 1.0912 5.6387
PGA_scaffold5__109_contigs__length_67248332 67248332 64231405 0.9551 3.9737
PGA_scaffold6__104_contigs__length_61759565 61759565 64103338 1.0379 7.1382
PGA_scaffold7__69_contigs__length_43120122 43120122 45996307 1.0667 3.4606
PGA_scaffold8__63_contigs__length_61151155 61151155 67015097 1.0959 3.9912
PGA_scaffold9__45_contigs__length_38581958 38581958 46920811 1.2161 10.2774
PGA_scaffold10__49_contigs__length_53961475 53961475 54672630 1.0132 3.1107
PGA_scaffold11__79_contigs__length_51449921 51449921 48524375 0.9431 3.941
PGA_scaffold12__71_contigs__length_50438331 50438331 58008705 1.1501 4.8388
PGA_scaffold13__52_contigs__length_44396874 44396874 47602343 1.0722 4.1622
PGA_scaffold14__91_contigs__length_45393038 45393038 63070384 1.3894 20.3313
PGA_scaffold15__101_contigs__length_47938513 47938513 42819577 0.8932 3.4677
PGA_scaffold16__33_contigs__length_31980953 31980953 37803357 1.1821 14.3232
PGA_scaffold17__51_contigs__length_34923512 34923512 38391893 1.0993 4.2905
PGA_scaffold18__69_contigs__length_27737463 27737463 27014826 0.9739 6.1144

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 12:54:07
    Generated by QualiMap v.2.2.1