Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 12,798,640
Mapped reads 12,798,640 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 12,798,640 / 100%
Mapped reads, first in pair 6,399,320 / 50%
Mapped reads, second in pair 6,399,320 / 50%
Mapped reads, both in pair 12,798,640 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 85.39
Duplicated reads (estimated) 4,528,070 / 35.38%
Duplication rate 33.64%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 417,304,426 / 38.3%
Number/percentage of C's 128,758,812 / 11.82%
Number/percentage of T's 416,052,058 / 38.18%
Number/percentage of G's 127,564,360 / 11.71%
Number/percentage of N's 76,115 / 0.01%
GC Percentage 23.52%

Coverage

Mean 1.159
Standard Deviation 7.0888

Mapping Quality

Mean Mapping Quality 23.67

Insert size

Mean 142.54
Standard Deviation 93.09
P25/Median/P75 75 / 118 / 183

Mismatches and indels

General error rate 18.69%
Mismatches 199,540,763
Insertions 1,427,045
Mapped reads with at least one insertion 9.77%
Deletions 1,306,891
Mapped reads with at least one deletion 9.24%
Homopolymer indels 48.8%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 109795430 1.2248 3.7135
PGA_scaffold2__36_contigs__length_69596280 69596280 87286178 1.2542 5.2323
PGA_scaffold3__111_contigs__length_57743597 57743597 69890712 1.2104 4.0257
PGA_scaffold4__129_contigs__length_65288255 65288255 74816635 1.1459 5.733
PGA_scaffold5__109_contigs__length_67248332 67248332 67449120 1.003 4.1826
PGA_scaffold6__104_contigs__length_61759565 61759565 67144589 1.0872 6.0751
PGA_scaffold7__69_contigs__length_43120122 43120122 48897568 1.134 3.7977
PGA_scaffold8__63_contigs__length_61151155 61151155 71669923 1.172 4.3332
PGA_scaffold9__45_contigs__length_38581958 38581958 49451472 1.2817 10.363
PGA_scaffold10__49_contigs__length_53961475 53961475 58724856 1.0883 3.4063
PGA_scaffold11__79_contigs__length_51449921 51449921 52229921 1.0152 4.5631
PGA_scaffold12__71_contigs__length_50438331 50438331 61850700 1.2263 5.1513
PGA_scaffold13__52_contigs__length_44396874 44396874 50951329 1.1476 4.3829
PGA_scaffold14__91_contigs__length_45393038 45393038 67373170 1.4842 20.9117
PGA_scaffold15__101_contigs__length_47938513 47938513 45347308 0.9459 3.6335
PGA_scaffold16__33_contigs__length_31980953 31980953 39473059 1.2343 13.3324
PGA_scaffold17__51_contigs__length_34923512 34923512 41022670 1.1746 4.1913
PGA_scaffold18__69_contigs__length_27737463 27737463 28767302 1.0371 6.2377

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 14:05:24
    Generated by QualiMap v.2.2.1