Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 15,001,974
Mapped reads 15,001,974 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 15,001,974 / 100%
Mapped reads, first in pair 7,500,987 / 50%
Mapped reads, second in pair 7,500,987 / 50%
Mapped reads, both in pair 15,001,974 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 84.17
Duplicated reads (estimated) 5,845,680 / 38.97%
Duplication rate 37.06%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 482,802,585 / 38.34%
Number/percentage of C's 148,189,857 / 11.77%
Number/percentage of T's 481,411,324 / 38.23%
Number/percentage of G's 146,744,107 / 11.65%
Number/percentage of N's 106,890 / 0.01%
GC Percentage 23.42%

Coverage

Mean 1.3391
Standard Deviation 7.3512

Mapping Quality

Mean Mapping Quality 24.2

Insert size

Mean 134.88
Standard Deviation 89.95
P25/Median/P75 71 / 110 / 170

Mismatches and indels

General error rate 18.51%
Mismatches 228,387,172
Insertions 1,572,228
Mapped reads with at least one insertion 9.19%
Deletions 1,468,556
Mapped reads with at least one deletion 8.87%
Homopolymer indels 48.82%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 128949325 1.4385 4.3703
PGA_scaffold2__36_contigs__length_69596280 69596280 101964813 1.4651 5.8132
PGA_scaffold3__111_contigs__length_57743597 57743597 80559553 1.3951 4.6311
PGA_scaffold4__129_contigs__length_65288255 65288255 85414167 1.3083 6.2976
PGA_scaffold5__109_contigs__length_67248332 67248332 78912341 1.1734 4.7548
PGA_scaffold6__104_contigs__length_61759565 61759565 76623389 1.2407 6.0803
PGA_scaffold7__69_contigs__length_43120122 43120122 57095504 1.3241 4.4571
PGA_scaffold8__63_contigs__length_61151155 61151155 82168642 1.3437 4.6467
PGA_scaffold9__45_contigs__length_38581958 38581958 57066876 1.4791 12.0156
PGA_scaffold10__49_contigs__length_53961475 53961475 68854273 1.276 4.1144
PGA_scaffold11__79_contigs__length_51449921 51449921 59092658 1.1485 4.7155
PGA_scaffold12__71_contigs__length_50438331 50438331 72147634 1.4304 6.0971
PGA_scaffold13__52_contigs__length_44396874 44396874 59160509 1.3325 5.3916
PGA_scaffold14__91_contigs__length_45393038 45393038 77233867 1.7014 21.1208
PGA_scaffold15__101_contigs__length_47938513 47938513 52196617 1.0888 4.3586
PGA_scaffold16__33_contigs__length_31980953 31980953 44880987 1.4034 10.0102
PGA_scaffold17__51_contigs__length_34923512 34923512 46937466 1.344 4.8052
PGA_scaffold18__69_contigs__length_27737463 27737463 32688643 1.1785 6.2126

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 13:00:32
    Generated by QualiMap v.2.2.1