Meaning of the Output from BBMap

Question

[madhu.9124]

Hi, I ran command , ./bbmap.sh in=ecoliReads1.fastq outm=mappedadd_ecoli.bam outu=unmapped2.fa ref=ecoliRef.fasta. The output that was printed was:

BBMap version 37.28
Retaining first best site only for ambiguous mappings.
NOTE:   Ignoring reference file because it already appears to have been processed.
NOTE:   If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1

Loaded Reference:   0.233 seconds.
Loading index for chunk 1-1, build 1
Generated Index:    0.681 seconds.
Analyzed Index:     1.900 seconds.
Could not find samtools.
Started output stream:  0.149 seconds.
Started output stream:  0.000 seconds.
Cleared Memory:     0.119 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 8 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7

   ------------------   Results   ------------------   

Genome:                 1
Key Length:             13
Max Indel:              16000
Minimum Score Ratio:    0.56
Mapping Mode:           normal
Reads Used:             143712  (42992527 bases)

Mapping:            26.545 seconds.
Reads/sec:          5413.82
kBases/sec:         1619.59


Read 1 data:        pct reads   num reads   pct bases      num bases

mapped:              99.6987%      143279    99.7236%       42873698
unambiguous:         99.6973%      143277    99.7222%       42873096
ambiguous:            0.0014%           2     0.0014%            602
low-Q discards:       0.0000%           0     0.0000%              0

perfect best site:    0.0000%           0     0.0000%              0
semiperfect site:     0.0000%           0     0.0000%              0

Match Rate:               NA           NA    96.3411%       41331109
Error Rate:          99.8780%      143279     3.6589%        1569695
Sub Rate:            99.8780%      143279     3.5904%        1540309
Del Rate:             3.1230%        4480     0.0632%          27118
Ins Rate:             0.8351%        1198     0.0053%           2268
N Rate:               0.0084%          12     0.0000%             12

Total time:         30.133 seconds.

So I would like to what the 99.6987% for the mapped mean. Kindly explain the meaning of that value. Any link or tutorial to support it would be appreciated.

Thanks Madhu

[GenoMax]

Exactly what it says. 99+% of your input reads (143279) mapped to the genome you are using. All (except 2) unambiguously.

Answer 1

[Hussain Ather]

Here's a tutorial https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/