Summary 

Globals

Reference size 942,353,201
Number of reads 10,406,202
Mapped reads 10,406,202 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 10,406,202 / 100%
Mapped reads, first in pair 5,203,101 / 50%
Mapped reads, second in pair 5,203,101 / 50%
Mapped reads, both in pair 10,406,202 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 91.15
Duplicated reads (estimated) 3,122,494 / 30.01%
Duplication rate 25.06%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 356,201,067 / 38%
Number/percentage of C's 114,208,645 / 12.18%
Number/percentage of T's 354,666,646 / 37.83%
Number/percentage of G's 112,411,222 / 11.99%
Number/percentage of N's 60,093 / 0.01%
GC Percentage 24.17%

Coverage

Mean 1.0003
Standard Deviation 8.4696

Mapping Quality

Mean Mapping Quality 19.32

Insert size

Mean 164.2
Standard Deviation 95.77
P25/Median/P75 97 / 132 / 203

Mismatches and indels

General error rate 21.48%
Mismatches 188,519,644
Insertions 4,082,483
Mapped reads with at least one insertion 22.72%
Deletions 2,468,319
Mapped reads with at least one deletion 17.95%
Homopolymer indels 39.14%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 90772537 1.0126 4.221
PGA_scaffold2__36_contigs__length_69596280 69596280 73247137 1.0525 5.2593
PGA_scaffold3__111_contigs__length_57743597 57743597 58929030 1.0205 4.2377
PGA_scaffold4__129_contigs__length_65288255 65288255 64656159 0.9903 10.2783
PGA_scaffold5__109_contigs__length_67248332 67248332 59906055 0.8908 5.2413
PGA_scaffold6__104_contigs__length_61759565 61759565 58670631 0.95 6.9604
PGA_scaffold7__69_contigs__length_43120122 43120122 41984159 0.9737 4.0442
PGA_scaffold8__63_contigs__length_61151155 61151155 60033092 0.9817 4.1734
PGA_scaffold9__45_contigs__length_38581958 38581958 45012577 1.1667 13.8521
PGA_scaffold10__49_contigs__length_53961475 53961475 50014896 0.9269 4.7249
PGA_scaffold11__79_contigs__length_51449921 51449921 45015247 0.8749 4.8824
PGA_scaffold12__71_contigs__length_50438331 50438331 53047475 1.0517 6.1566
PGA_scaffold13__52_contigs__length_44396874 44396874 43700117 0.9843 5.0133
PGA_scaffold14__91_contigs__length_45393038 45393038 59044733 1.3007 22.9321
PGA_scaffold15__101_contigs__length_47938513 47938513 39807183 0.8304 3.9466
PGA_scaffold16__33_contigs__length_31980953 31980953 36208232 1.1322 16.9796
PGA_scaffold17__51_contigs__length_34923512 34923512 35978612 1.0302 5.7434
PGA_scaffold18__69_contigs__length_27737463 27737463 26601562 0.959 7.7606

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