Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,072,532
Mapped reads 12,072,532 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,072,532 / 100%
Mapped reads, first in pair 6,036,266 / 50%
Mapped reads, second in pair 6,036,266 / 50%
Mapped reads, both in pair 12,072,532 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 86.51
Duplicated reads (estimated) 4,252,177 / 35.22%
Duplication rate 33.34%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 398,756,007 / 38.29%
Number/percentage of C's 123,401,473 / 11.85%
Number/percentage of T's 397,382,381 / 38.16%
Number/percentage of G's 121,893,218 / 11.7%
Number/percentage of N's 60,161 / 0.01%
GC Percentage 23.55%

Coverage

Mean 1.1076
Standard Deviation 7.6795

Mapping Quality

Mean Mapping Quality 24.03

Insert size

Mean 140.59
Standard Deviation 89.43
P25/Median/P75 77 / 117 / 177

Mismatches and indels

General error rate 18.63%
Mismatches 190,068,974
Insertions 1,315,534
Mapped reads with at least one insertion 9.54%
Deletions 1,228,641
Mapped reads with at least one deletion 9.22%
Homopolymer indels 48.97%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 105495800 1.1768 4.0176
PGA_scaffold2__36_contigs__length_69596280 69596280 84180499 1.2096 5.5811
PGA_scaffold3__111_contigs__length_57743597 57743597 66414636 1.1502 3.9999
PGA_scaffold4__129_contigs__length_65288255 65288255 70786366 1.0842 5.822
PGA_scaffold5__109_contigs__length_67248332 67248332 64870036 0.9646 4.247
PGA_scaffold6__104_contigs__length_61759565 61759565 64425901 1.0432 7.8409
PGA_scaffold7__69_contigs__length_43120122 43120122 46051439 1.068 3.6913
PGA_scaffold8__63_contigs__length_61151155 61151155 67667744 1.1066 4.3129
PGA_scaffold9__45_contigs__length_38581958 38581958 47436423 1.2295 10.7527
PGA_scaffold10__49_contigs__length_53961475 53961475 56475744 1.0466 3.4571
PGA_scaffold11__79_contigs__length_51449921 51449921 49350951 0.9592 4.5073
PGA_scaffold12__71_contigs__length_50438331 50438331 59370342 1.1771 5.2441
PGA_scaffold13__52_contigs__length_44396874 44396874 48675244 1.0964 4.5195
PGA_scaffold14__91_contigs__length_45393038 45393038 64529694 1.4216 21.3809
PGA_scaffold15__101_contigs__length_47938513 47938513 42921783 0.8954 3.7123
PGA_scaffold16__33_contigs__length_31980953 31980953 38398089 1.2007 17.8216
PGA_scaffold17__51_contigs__length_34923512 34923512 38816959 1.1115 4.7287
PGA_scaffold18__69_contigs__length_27737463 27737463 27877237 1.005 6.7968

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 13:15:01
    Generated by QualiMap v.2.2.1