Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 11,167,572
Mapped reads 11,167,572 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 11,167,572 / 100%
Mapped reads, first in pair 5,583,786 / 50%
Mapped reads, second in pair 5,583,786 / 50%
Mapped reads, both in pair 11,167,572 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 89.54
Duplicated reads (estimated) 3,355,388 / 30.05%
Duplication rate 25.3%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 375,667,228 / 38%
Number/percentage of C's 120,070,228 / 12.15%
Number/percentage of T's 374,262,174 / 37.86%
Number/percentage of G's 118,629,144 / 12%
Number/percentage of N's 63,759 / 0.01%
GC Percentage 24.14%

Coverage

Mean 1.0548
Standard Deviation 8.3755

Mapping Quality

Mean Mapping Quality 19.55

Insert size

Mean 166.13
Standard Deviation 98.21
P25/Median/P75 96 / 133 / 207

Mismatches and indels

General error rate 21.36%
Mismatches 198,097,398
Insertions 4,175,258
Mapped reads with at least one insertion 22.02%
Deletions 2,564,341
Mapped reads with at least one deletion 17.5%
Homopolymer indels 39.55%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 96544125 1.077 4.0881
PGA_scaffold2__36_contigs__length_69596280 69596280 76894399 1.1049 5.4218
PGA_scaffold3__111_contigs__length_57743597 57743597 62114573 1.0757 4.3399
PGA_scaffold4__129_contigs__length_65288255 65288255 68029624 1.042 9.8616
PGA_scaffold5__109_contigs__length_67248332 67248332 63355511 0.9421 5.2912
PGA_scaffold6__104_contigs__length_61759565 61759565 61598874 0.9974 6.6519
PGA_scaffold7__69_contigs__length_43120122 43120122 44253683 1.0263 3.9277
PGA_scaffold8__63_contigs__length_61151155 61151155 63914461 1.0452 4.4263
PGA_scaffold9__45_contigs__length_38581958 38581958 46719419 1.2109 13.7091
PGA_scaffold10__49_contigs__length_53961475 53961475 52763677 0.9778 4.6433
PGA_scaffold11__79_contigs__length_51449921 51449921 47417071 0.9216 4.852
PGA_scaffold12__71_contigs__length_50438331 50438331 55825534 1.1068 6.1407
PGA_scaffold13__52_contigs__length_44396874 44396874 46284855 1.0425 5.2577
PGA_scaffold14__91_contigs__length_45393038 45393038 62133432 1.3688 22.7115
PGA_scaffold15__101_contigs__length_47938513 47938513 42323323 0.8829 3.9098
PGA_scaffold16__33_contigs__length_31980953 31980953 37966267 1.1872 16.6996
PGA_scaffold17__51_contigs__length_34923512 34923512 38141711 1.0921 5.5564
PGA_scaffold18__69_contigs__length_27737463 27737463 27715846 0.9992 7.9116

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 16:56:30
    Generated by QualiMap v.2.2.1