Table 4.
Summary of reads mapped to reference genome.
| Sample name | cont1 | cont2 | infect1 | infect2 |
|---|---|---|---|---|
| The effective reads | 112941906 (100%) | 123138246 (100%) | 86025798 (100%) | 107088594 (100%) |
| Total mapped | 5194592 (4.60%) | 3683147 (2.99%) | 4047510 (4.70%) | 3269932 (3.05%) |
| Multiple mapped | 550374 (0.49%) | 253166 (0.21%) | 492395 (0.57%) | 411581 (0.38%) |
| Uniquely mapped | 4644218 (4.11%) | 3429981 (2.79%) | 3555115 (4.13%) | 2858351 (2.67%) |
| Read1 mapped | 2600145 (2.30%) | 1843109 (1.50%) | 2022180 (2.35%) | 1633528 (1.53%) |
| Read2 mapped | 2594447 (2.30%) | 1840038 (1.49%) | 2,025,330 (2.35%) | 1636404 (1.53%) |
| Reads map to “+” | 2,599,952 (2.30%) | 1842749 (1.50%) | 2025784 (2.35%) | 1636402 (1.53%) |
| Reads map to “-” | 2594640 (2.30%) | 1840398 (1.49%) | 2,021,726 (2.35%) | 1633530 (1.53%) |
| Reads mapped in proper pairs | 4815452 (4.26%) | 3470648 (2.82%) | 3800530 (4.42%) | 3059418 (2.86%) |
The effective reads: the remaining number of clean reads after removing rRNA reads will be used for subsequent genome alignment; total mapped: the number of sequencing sequences that can be aligned on the genome; multiple mapped: the number of sequencing sequences with multiple alignment positions on the sequence of reference; uniquely mapped: the number of sequencing sequences with unique alignment positions on the reference sequence; read-1, read-2 mapped: pair-end sequence, whose two parts that can be located on the number of genome, respectively; the statistical ratio of the two parts should be roughly the same; reads map to “+”: the number of reads aligned to the positive strand of the genome; reads map to “-”: the number of reads aligned to the genome on the negative strand; reads mapped in proper pairs: the relative distance of the pair end sequence mapping to the genome conforms to the length distribution of the sequenced fragments.