- Cutadapt - Illumina adaptor removal, quality trimming of bases with Phred score below 30, with a minimum read length of 50bp
Trimmeddirectory
- SortMeRNA - Removal of rRNA sequences, based on the S. marinoi genome (and some manual checking of rRNA boundaries)
rRNA_Filterdirectory
- PRINSEQ - Trimming of long (10+) polyA/T tails from reads, and removal of reads subsequently shorter than 50bp
PolyA_Removaldirectory
| | | | | PreQC (P18257) | Post-QC (adapter removal, Q >=30, min len 50) | Post-rRNA removal | Post-polyA/T removal (10+ A/T) + min len 50 |
| Sample ID | Strain | Dormancy | Batch | Read pairs | Bases | Read pairs | Bases | Read pairs | Bases | Read pairs | Bases |
|---|---|---|---|---|---|---|---|---|---|---|---|
| P18257_101 | R05 | 0 | B | 27,630,558 | 8,344,428,516 | 27,144,843 (98.2%) | 8,033,362,479 (96.3%) | 26,974,845 (97.6%) | 7,983,087,553 (95.7%) | 26,964,997 (97.6%) | 7,976,350,166 (95.6%) |
| P18257_102 | R05 | 0 | B | 31,258,119 | 9,439,951,938 | 30,818,260 (98.6%) | 9,122,800,288 (96.6%) | 30,541,148 (97.7%) | 9,040,813,847 (95.8%) | 30,523,870 (97.7%) | 9,029,988,173 (95.7%) |
| P18257_103 | R05 | 0 | B | 24,416,814 | 7,373,877,828 | 24,191,350 (99.1%) | 7,151,088,874 (97.0%) | 23,955,679 (98.1%) | 7,081,533,589 (96.0%) | 23,951,781 (98.1%) | 7,078,789,179 (96.0%) |
| P18257_104 | GF04 | 0 | A | 13,210,989 | 3,989,718,678 | 13,073,721 (99.0%) | 3,781,270,330 (94.8%) | 12,775,005 (96.7%) | 3,694,579,533 (92.6%) | 12,772,847 (96.7%) | 3,692,184,373 (92.5%) |
| P18257_105 | GF04 | 0 | A | 13,872,256 | 4,189,421,312 | 13,538,306 (97.6%) | 3,986,852,749 (95.2%) | 13,312,805 (96.0%) | 3,920,244,221 (93.6%) | 13,304,855 (95.9%) | 3,913,437,795 (93.4%) |
| P18257_106 | GF04 | 0 | B | 24,433,872 | 7,379,029,344 | 24,040,310 (98.4%) | 7,142,367,067 (96.8%) | 23,740,340 (97.2%) | 7,053,287,742 (95.6%) | 23,726,574 (97.1%) | 7,044,303,587 (95.5%) |
| P18257_107 | R05 | 49 | A | 14,720,617 | 4,445,626,334 | 14,474,824 (98.3%) | 4,257,928,965 (95.8%) | 14,417,296 (97.9%) | 4,240,972,570 (95.4%) | 14,406,061 (97.9%) | 4,233,495,769 (95.2%) |
| P18257_108 | R05 | 49 | B | 19,216,751 | 5,803,458,802 | 19,068,567 (99.2%) | 5,530,694,142 (95.3%) | 19,018,224 (99.0%) | 5,516,177,975 (95.0%) | 19,016,128 (99.0%) | 5,514,449,907 (95.0%) |
| P18257_109 | R05 | 49 | A | 18,567,539 | 5,607,396,778 | 18,365,406 (98.9%) | 5,397,869,931 (96.3%) | 18,278,788 (98.4%) | 5,372,350,359 (95.8%) | 18,273,669 (98.4%) | 5,368,064,327 (95.7%) |
| P18257_111 | GF04 | 49 | A | 17,267,165 | 5,214,683,830 | 17,057,781 (98.8%) | 5,023,794,391 (96.3%) | 16,986,496 (98.4%) | 5,002,762,433 (95.9%) | 16,978,527 (98.3%) | 4,997,325,288 (95.8%) |
| P18257_112 | GF04 | 49 | B | 19,464,348 | 5,878,233,096 | 19,218,186 (98.7%) | 5,606,189,106 (95.4%) | 19,151,354 (98.4%) | 5,586,762,164 (95.0%) | 19,149,435 (98.4%) | 5,584,984,846 (95.0%) |
| P18257_113 | R05 | 56 | A | 22,954,250 | 6,932,183,500 | 22,649,094 (98.7%) | 6,655,060,871 (96.0%) | 22,534,231 (98.2%) | 6,621,227,730 (95.5%) | 22,528,954 (98.1%) | 6,616,044,298 (95.4%) |
| P18257_114 | R05 | 56 | B | 23,357,124 | 7,053,851,448 | 22,988,810 (98.4%) | 6,811,154,154 (96.6%) | 22,922,118 (98.1%) | 6,791,420,686 (96.3%) | 22,912,575 (98.1%) | 6,784,567,987 (96.2%) |
| P18257_115 | R05 | 56 | B | 29,562,954 | 8,928,012,108 | 28,996,076 (98.1%) | 8,650,159,079 (96.9%) | 28,899,615 (97.8%) | 8,621,388,035 (96.6%) | 28,889,541 (97.7%) | 8,613,988,084 (96.5%) |
| P18257_116 | GF04 | 56 | A | 18,867,927 | 5,698,113,954 | 18,662,326 (98.9%) | 5,505,192,930 (96.6%) | 18,558,514 (98.4%) | 5,474,504,766 (96.1%) | 18,554,107 (98.3%) | 5,470,827,738 (96.0%) |
| P18257_117 | GF04 | 56 | A | 20,741,254 | 6,263,858,708 | 20,463,587 (98.7%) | 6,024,219,192 (96.2%) | 20,384,068 (98.3%) | 6,000,751,401 (95.8%) | 20,377,484 (98.2%) | 5,995,524,799 (95.7%) |
| P18257_118 | GF04 | 56 | A | 19,355,885 | 5,845,477,270 | 19,101,935 (98.7%) | 5,626,692,028 (96.3%) | 19,017,331 (98.3%) | 5,601,705,423 (95.8%) | 19,009,878 (98.2%) | 5,596,071,677 (95.7%) |
| P18257_119 | R05 | 72 | B | 30,031,969 | 9,069,654,638 | 29,657,044 (98.8%) | 8,791,638,638 (96.9%) | 29,528,552 (98.3%) | 8,753,580,891 (96.5%) | 29,522,973 (98.3%) | 8,749,202,679 (96.5%) |
| P18257_120 | R05 | 72 | B | 28,041,178 | 8,468,435,756 | 27,758,092 (99.0%) | 8,230,318,859 (97.2%) | 27,654,083 (98.6%) | 8,199,512,629 (96.8%) | 27,649,975 (98.6%) | 8,196,054,531 (96.8%) |
| P18257_121 | R05 | 72 | A | 15,886,811 | 4,797,816,922 | 15,697,685 (98.8%) | 4,615,653,814 (96.2%) | 15,620,578 (98.3%) | 4,592,934,324 (95.7%) | 15,615,210 (98.3%) | 4,588,803,208 (95.6%) |
| P18257_122 | GF04 | 72 | A | 24,216,259 | 7,313,310,218 | 23,896,432 (98.7%) | 7,046,053,665 (96.3%) | 23,790,785 (98.2%) | 7,014,817,175 (95.9%) | 23,783,152 (98.2%) | 7,008,495,322 (95.8%) |
| P18257_123 | GF04 | 72 | A | 22,383,156 | 6,759,713,112 | 21,890,445 (97.8%) | 6,461,833,191 (95.6%) | 21,756,363 (97.2%) | 6,422,141,265 (95.0%) | 21,749,368 (97.2%) | 6,415,622,743 (94.9%) |
| P18257_124 | GF04 | 72 | A | 20,816,984 | 6,286,729,168 | 20,598,902 (99.0%) | 6,084,541,193 (96.8%) | 20,467,946 (98.3%) | 6,045,794,824 (96.2%) | 20,464,516 (98.3%) | 6,042,500,779 (96.1%) |
| P18257_125 | R05 | 91 | B | 28,159,154 | 8,504,064,508 | 27,843,636 (98.9%) | 8,256,547,626 (97.1%) | 27,739,519 (98.5%) | 8,225,707,220 (96.7%) | 27,733,409 (98.5%) | 8,220,958,823 (96.7%) |
| P18257_126 | R05 | 91 | B | 22,840,908 | 6,897,954,216 | 22,584,366 (98.9%) | 6,640,246,983 (96.3%) | 22,517,394 (98.6%) | 6,620,589,618 (96.0%) | 22,510,027 (98.6%) | 6,615,642,062 (95.9%) |
| P18257_127 | R05 | 91 | B | 23,252,759 | 7,022,333,218 | 23,002,175 (98.9%) | 6,796,607,643 (96.8%) | 22,920,447 (98.6%) | 6,772,503,218 (96.4%) | 22,915,074 (98.5%) | 6,768,427,744 (96.4%) |
| P18257_128 | GF04 | 91 | A | 21,362,737 | 6,451,546,574 | 20,845,412 (97.6%) | 6,139,053,895 (95.2%) | 20,728,285 (97.0%) | 6,104,489,730 (94.6%) | 20,711,678 (97.0%) | 6,092,560,598 (94.4%) |
| P18257_129 | GF04 | 91 | A | 12,919,980 | 3,901,833,960 | 12,758,893 (98.8%) | 3,722,553,788 (95.4%) | 12,696,548 (98.3%) | 3,704,308,564 (94.9%) | 12,693,456 (98.2%) | 3,701,656,148 (94.9%) |
| P18257_130 | GF04 | 91 | A | 19,958,698 | 6,027,526,796 | 19,636,128 (98.4%) | 5,790,853,096 (96.1%) | 19,485,697 (97.6%) | 5,746,365,180 (95.3%) | 19,478,663 (97.6%) | 5,740,434,696 (95.2%) |
| P18257_131 | R05 | 126 | B | 26,983,968 | 8,149,158,336 | 26,583,745 (98.5%) | 7,891,014,376 (96.8%) | 26,497,390 (98.2%) | 7,865,420,038 (96.5%) | 26,493,679 (98.2%) | 7,862,495,353 (96.5%) |
| P18257_132 | R05 | 126 | B | 25,860,678 | 7,809,924,756 | 25,406,414 (98.2%) | 7,535,272,249 (96.5%) | 25,328,021 (97.9%) | 7,512,034,928 (96.2%) | 25,318,991 (97.9%) | 7,504,609,702 (96.1%) |
| P18257_133 | R05 | 126 | B | 38,930,680 | 11,757,065,360 | 38,427,319 (98.7%) | 11,362,696,080 (96.6%) | 38,288,455 (98.4%) | 11,321,607,912 (96.3%) | 38,280,905 (98.3%) | 11,314,683,711 (96.2%) |
| P18257_134 | GF04 | 126 | A | 23,126,369 | 6,984,163,438 | 22,648,206 (97.9%) | 6,649,819,310 (95.2%) | 22,535,078 (97.4%) | 6,616,494,050 (94.7%) | 22,522,224 (97.4%) | 6,606,669,634 (94.6%) |
| P18257_135 | GF04 | 126 | A | 21,408,346 | 6,465,320,492 | 21,071,978 (98.4%) | 6,171,038,718 (95.4%) | 20,972,510 (98.0%) | 6,141,831,426 (95.0%) | 20,961,230 (97.9%) | 6,133,680,704 (94.9%) |
| P18257_136 | GF04 | 126 | A | 22,314,449 | 6,738,963,598 | 22,014,880 (98.7%) | 6,469,652,131 (96.0%) | 21,914,506 (98.2%) | 6,440,089,770 (95.6%) | 21,910,686 (98.2%) | 6,436,540,333 (95.5%) |
| P18257_138 | R05 | 189 | A | 25,575,070 | 7,723,671,140 | 24,986,981 (97.7%) | 7,329,164,496 (94.9%) | 24,863,742 (97.2%) | 7,292,918,569 (94.4%) | 24,848,957 (97.2%) | 7,281,441,145 (94.3%) |
| P18257_139 | R05 | 189 | A | 49,315,597 | 14,893,310,294 | 48,422,853 (98.2%) | 14,240,998,166 (95.6%) | 48,169,705 (97.7%) | 14,166,356,962 (95.1%) | 48,136,574 (97.6%) | 14,142,703,907 (95.0%) |
| P18257_140 | GF04 | 189 | A | 45,487,468 | 13,737,215,336 | 44,848,029 (98.6%) | 13,299,814,085 (96.8%) | 44,619,897 (98.1%) | 13,232,081,054 (96.3%) | 44,606,533 (98.1%) | 13,220,639,240 (96.2%) |
| P18257_141 | GF04 | 189 | A | 21,787,580 | 6,579,849,160 | 21,343,483 (98.0%) | 6,263,313,903 (95.2%) | 21,249,637 (97.5%) | 6,235,717,798 (94.8%) | 21,235,628 (97.5%) | 6,225,567,790 (94.6%) |
| P18257_201 | GF04 | 49 | A | 9,637,282 | 2,910,459,164 | 9,420,039 (97.7%) | 2,740,619,346 (94.2%) | 9,380,713 (97.3%) | 2,729,146,094 (93.8%) | 9,372,664 (97.3%) | 2,723,315,198 (93.6%) |
| ------------ | -------- | ---------- | ------- | ------------- | ----------------- | --------------------- | ------------------------- | --------------------- | ------------------------- | --------------------- | ------------------------- |
| Total | - | - | - | 939,196,502 | 283,637,343,604 | 925,196,519 (98.5%) | 272,836,001,827 (96.2%) | 920,193,708 (98.0%) | 271,360,013,266 (95.7%) | 919,856,855 (97.9%) | 271,103,104,043 (95.6%) |