lakhujanivijay/HISAT_stats.md

## HISAT_stats.md

      
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              HISAT_stats.md
            
          
    Explanation of HISAT2 summary statistics

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).

The below explanation was originally posted by me on biostars.org 😎

The summary looks like this
HISAT2 summary stats:
            Total pairs: 11587225
                    Aligned concordantly or discordantly 0 time: 4464083 (38.53%)
                    Aligned concordantly 1 time: 2195620 (18.95%)
                    Aligned concordantly >1 times: 4877336 (42.09%)
                    Aligned discordantly 1 time: 50186 (0.43%)
            Total unpaired reads: 8928166
                    Aligned 0 time: 8019048 (89.82%)
                    Aligned 1 time: 304653 (3.41%)
                    Aligned >1 times: 604465 (6.77%)
            Overall alignment rate: 65.40%

Description

1. Total pairs: 11587225
Total reads = 11587225 * 2 = 23174450 (matches total number of reads in the sample)
2. Aligned concordantly or discordantly 0 time: 4464083 (38.53%)
These are unmapped reads :  4464083 * 2 (paired end) = 8928166
 ( 8928166 /  23174450 (Total reads) ) * 100 ~ 38.53%

3. Aligned concordantly 1 time: 2195620 (18.95%)
These are uniquely mapped reads : 2195620 * 2 (paired end) = 4391240
( 4391240 /  23174450 (Total reads) ) * 100 ~ 18.95%

4. Aligned concordantly >1 times: 4877336 (42.09%)
These are multi mapped reads : 4877336 * 2  = 9754672
( 9754672 /  23174450 (Total reads) ) * 100 ~ 42.09%

5.Aligned discordantly 1 time: 50186 (0.43%)
Discordant aligned : 50186 * 2 = 100372
( 100372 /  23174450 (Total reads) ) * 100 ~ 0.43%

6. Total unpaired reads: 8928166
These are not paired reads


Aligned 0 time: 8019048 (89.82%)
(8019048 / 8928166 ) * 100 = 89.82%  i.e. 89% of the unpaired reads did not align at all


Aligned 1 time: 304653 (3.41%)
(304653 / 8928166 ) * 100 = 3.41%  i.e. 3.41% of the unpaired reads aligned once


Aligned >1 times: 604465 (6.77%)
(604465 / 8928166 ) * 100 = 6.77%  i.e. 6.77% of the unpaired reads are multi mapped


7. Overall alignment rate: 65.40%
Calculation as explained below
PAIRED READS

Aligned concordantly 1 time: (2195620 * 2 = 4391240)
Aligned concordantly >1 times: (4877336 * 2  = 9754672)
Aligned discordantly 1 time: (50186 * 2 = 100372)
UNPAIRED READS

Aligned 1 time: 304653
Aligned >1 times: 604465

Total = 4391240 + 9754672 +  100372 +  304653 +  604465 = 15155402
Overall Alignment Rate = (15155402 / 23174450) * 100 = 65.40%