TABLE 2.
Overview of individual metagenomic sequence data from gadoid intestinesa
| Sample | Raw reads | After quality trimming/filtering (%) | Host DNA (%) | Bacterial DNA (%) | Final reads |
|---|---|---|---|---|---|
| NCC_01 | 10,883,740 | 85.9 | 87.3 | 12.7 | 1,187,649 |
| NCC_02 | 11,140,950 | 87.9 | 62.2 | 37.8 | 3,699,538 |
| NCC_03 | 9,891,322 | 90.2 | 41.2 | 58.8 | 5,249,515 |
| NCC_04 | 10,587,865 | 86.9 | 85.2 | 14.8 | 1,364,663 |
| NCC_05 | 8,423,091 | 89.1 | 57.7 | 42.3 | 3,171,737 |
| NCC_06 | 10,879,319 | 89.6 | 30.5 | 69.5 | 6,772,948 |
| NCC_07 | 10,082,237 | 91.8 | 31.3 | 68.7 | 6,361,506 |
| NCC_08 | 9,114,703 | 87.3 | 80.5 | 19.5 | 1,549,210 |
| NCC_09 | 11,105,189 | 89.1 | 62.2 | 37.8 | 3,733,846 |
| NCC_10 | 11,140,743 | 84.7 | 86.0 | 14.0 | 1,320,875 |
| NEAC_01 | 13,120,072 | 89.7 | 53.6 | 46.4 | 5,463,098 |
| NEAC_02 | 12,119,926 | 89.6 | 56.8 | 43.2 | 4,687,565 |
| NEAC_03 | 11,981,093 | 89.2 | 54.4 | 45.6 | 4,869,722 |
| NEAC_04 | 12,618,529 | 91.1 | 33.5 | 66.5 | 7,646,256 |
| NEAC_05 | 12,154,047 | 87.6 | 74.2 | 25.8 | 2,747,042 |
| NEAC_06 | 13,883,762 | 88.4 | 59.5 | 40.5 | 4,971,507 |
| NEAC_07 | 12,149,049 | 89.1 | 56.9 | 43.1 | 4,666,533 |
| NEAC_08 | 11,861,852 | 88.7 | 64.0 | 36.0 | 3,787,155 |
| NEAC_09 | 11,131,413 | 85.7 | 75.1 | 24.9 | 2,378,591 |
| NEAC_10 | 15,483,018 | 83.7 | 82.9 | 17.1 | 2,221,214 |
| OO_cod_01 | 8,047,125 | 83.7 | 85.9 | 14.1 | 949,039 |
| IO_cod_01 | 9,716,392 | 90.2 | 43.7 | 56.3 | 4,937,260 |
| NP_01 | 15,621,734 | 84.7 | 51.6 | 48.4 | 6,400,120 |
| NP_02 | 16,548,297 | 90.2 | 18.1 | 81.9 | 12,224,903 |
| NP_03 | 16,608,312 | 78.3 | 72.6 | 27.4 | 3,568,206 |
| NP_04 | 13,459,929 | 83.0 | 61.5 | 38.5 | 4,300,178 |
| PC_01 | 10,743,586 | 87.7 | 30.5 | 69.5 | 6,550,868 |
| PC_02 | 18,982,339 | 81.0 | 29.6 | 70.4 | 10,833,201 |
| PC_03 | 9,420,298 | 84.1 | 54.9 | 45.1 | 3,568,861 |
| PC_04 | 9,623,591 | 87.7 | 30.0 | 70.0 | 5,908,283 |
| PC_05 | 19,630,680 | 77.7 | 55.0 | 45.0 | 6,861,474 |
| NSP_01 | 14,283,994 | 73.2 | 67.5 | 32.5 | 3,396,962 |
| NSP_02 | 14,527,770 | 76.3 | 63.8 | 36.2 | 4,008,926 |
| NSP_03 | 15,261,446 | 80.9 | 66.6 | 33.4 | 4,123,131 |
| Total: | 422,227,413 | 155,481,582 | |||
| Mean: | 12,418,453 | 86.0 | 57.8 | 42.2 |
a
PhiX- and human-derived DNA sequences represented a negligible proportion and were excluded from the table. On average, 42.2% of the quality filtered reads per sample were used for microbiome analysis. (For further details, see Table S7.)