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Commit 0a8b3f0a authored by eortega's avatar eortega
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*.gz
*.fq.gz
*.fasta
*.fna
*.bt2
*.fna
*.fna.fai
*.gbff.gz
*.gff.gz
*.faa.gz
*.sam
*.bam
*.bai
*.vcf
*.bcf
*.png
*.csv
*.zip
*multiqc.log
*multiqc_data.json
*multiqc_fastqc.txt
*multiqc_general_stats.txt
*multiqc_sources.txt
phages/data/refs/README.txt 0 → 100644
View file @ 0a8b3f0a
Streptococcus thermophilus
Sequences downloaded from:
https://www.ncbi.nlm.nih.gov/genome/?term=txid1268061[Organism:noexp]
Files downloaded:
GCF_000253395.1_ASM25339v1_genomic.fna.gz
GCF_000253395.1_ASM25339v1_genomic.gff.gz
GCF_000253395.1_ASM25339v1_genomic.gbff.gz
GCF_000253395.1_ASM25339v1_protein.faa.gz
Date downloaded:
20190524
phages/data/refs/Sv2972/NC_007019.1.gb 0 → 100644
View file @ 0a8b3f0a
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phages/data/refs/sv_dl_notes 0 → 100644
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Streptococcus phage 2972
Sequences downloaded from:
https://www.ncbi.nlm.nih.gov/nuccore/NC_007019.1?report=fasta
Files downloaded:
NC_007019.1.fasta
NC_007019.1.gb
Date downloaded:
20190524
phages/data/summary_trimm_Other 0 → 100644
View file @ 0a8b3f0a
2972_S17
Input Read Pairs: 274182
Both Surviving Reads: 248778
Both Surviving Read Percent: 90.73
Forward Only Surviving Reads: 10255
Forward Only Surviving Read Percent: 3.74
Reverse Only Surviving Reads: 6338
Reverse Only Surviving Read Percent: 2.31
Dropped Reads: 8811
Dropped Read Percent: 3.21
####
A10-A_S16
Input Read Pairs: 229447
Both Surviving Reads: 206833
Both Surviving Read Percent: 90.14
Forward Only Surviving Reads: 9283
Forward Only Surviving Read Percent: 4.05
Reverse Only Surviving Reads: 4752
Reverse Only Surviving Read Percent: 2.07
Dropped Reads: 8579
Dropped Read Percent: 3.74
####
A7-A_S8
Input Read Pairs: 133220
Both Surviving Reads: 118074
Both Surviving Read Percent: 88.63
Forward Only Surviving Reads: 6747
Forward Only Surviving Read Percent: 5.06
Reverse Only Surviving Reads: 2328
Reverse Only Surviving Read Percent: 1.75
Dropped Reads: 6071
Dropped Read Percent: 4.56
####
A8-C_S12
Input Read Pairs: 99498
Both Surviving Reads: 88652
Both Surviving Read Percent: 89.10
Forward Only Surviving Reads: 5142
Forward Only Surviving Read Percent: 5.17
Reverse Only Surviving Reads: 1423
Reverse Only Surviving Read Percent: 1.43
Dropped Reads: 4281
Dropped Read Percent: 4.30
####
A9-A_S13
Input Read Pairs: 357640
Both Surviving Reads: 310615
Both Surviving Read Percent: 86.85
Forward Only Surviving Reads: 27600
Forward Only Surviving Read Percent: 7.72
Reverse Only Surviving Reads: 4094
Reverse Only Surviving Read Percent: 1.14
Dropped Reads: 15331
Dropped Read Percent: 4.29
####
B7-A_S9
Input Read Pairs: 96990
Both Surviving Reads: 86503
Both Surviving Read Percent: 89.19
Forward Only Surviving Reads: 4276
Forward Only Surviving Read Percent: 4.41
Reverse Only Surviving Reads: 2160
Reverse Only Surviving Read Percent: 2.23
Dropped Reads: 4051
Dropped Read Percent: 4.18
####
B8-B_S14
Input Read Pairs: 151881
Both Surviving Reads: 127388
Both Surviving Read Percent: 83.87
Forward Only Surviving Reads: 16531
Forward Only Surviving Read Percent: 10.88
Reverse Only Surviving Reads: 1330
Reverse Only Surviving Read Percent: 0.88
Dropped Reads: 6632
Dropped Read Percent: 4.37
####
B9-B_S10
Input Read Pairs: 99400
Both Surviving Reads: 85707
Both Surviving Read Percent: 86.22
Forward Only Surviving Reads: 7935
Forward Only Surviving Read Percent: 7.98
Reverse Only Surviving Reads: 1030
Reverse Only Surviving Read Percent: 1.04
Dropped Reads: 4728
Dropped Read Percent: 4.76
####
C2-B_S11
Input Read Pairs: 199684
Both Surviving Reads: 172964
Both Surviving Read Percent: 86.62
Forward Only Surviving Reads: 15131
Forward Only Surviving Read Percent: 7.58
Reverse Only Surviving Reads: 2061
Reverse Only Surviving Read Percent: 1.03
Dropped Reads: 9528
Dropped Read Percent: 4.77
####
C3-E_S7
Input Read Pairs: 114733
Both Surviving Reads: 102160
Both Surviving Read Percent: 89.04
Forward Only Surviving Reads: 5982
Forward Only Surviving Read Percent: 5.21
Reverse Only Surviving Reads: 1880
Reverse Only Surviving Read Percent: 1.64
Dropped Reads: 4711
Dropped Read Percent: 4.11
####
C4-B_S15
Input Read Pairs: 215278
Both Surviving Reads: 168480
Both Surviving Read Percent: 78.26
Forward Only Surviving Reads: 34692
Forward Only Surviving Read Percent: 16.11
Reverse Only Surviving Reads: 906
Reverse Only Surviving Read Percent: 0.42
Dropped Reads: 11200
Dropped Read Percent: 5.20
####
C6-C_S6
Input Read Pairs: 45
Both Surviving Reads: 12
Both Surviving Read Percent: 26.67
Forward Only Surviving Reads: 20
Forward Only Surviving Read Percent: 44.44
Reverse Only Surviving Reads: 1
Reverse Only Surviving Read Percent: 2.22
Dropped Reads: 12
Dropped Read Percent: 26.67
####
C7-A_S5
Input Read Pairs: 124291
Both Surviving Reads: 113190
Both Surviving Read Percent: 91.07
Forward Only Surviving Reads: 4302
Forward Only Surviving Read Percent: 3.46
Reverse Only Surviving Reads: 2390
Reverse Only Surviving Read Percent: 1.92
Dropped Reads: 4409
Dropped Read Percent: 3.55
####
C8-A_S2
Input Read Pairs: 105225
Both Surviving Reads: 90251
Both Surviving Read Percent: 85.77
Forward Only Surviving Reads: 8620
Forward Only Surviving Read Percent: 8.19
Reverse Only Surviving Reads: 1050
Reverse Only Surviving Read Percent: 1.00
Dropped Reads: 5304
Dropped Read Percent: 5.04
####
CTRL1_S25
Input Read Pairs: 189
Both Surviving Reads: 86
Both Surviving Read Percent: 45.50
Forward Only Surviving Reads: 26
Forward Only Surviving Read Percent: 13.76
Reverse Only Surviving Reads: 3
Reverse Only Surviving Read Percent: 1.59
Dropped Reads: 74
Dropped Read Percent: 39.15
####
CTRL2_S96
Input Read Pairs: 58
Both Surviving Reads: 24
Both Surviving Read Percent: 41.38
Forward Only Surviving Reads: 20
Forward Only Surviving Read Percent: 34.48
Reverse Only Surviving Reads: 1
Reverse Only Surviving Read Percent: 1.72
Dropped Reads: 13
Dropped Read Percent: 22.41
####
D1-D_S3
Input Read Pairs: 80922
Both Surviving Reads: 64820
Both Surviving Read Percent: 80.10
Forward Only Surviving Reads: 11481
Forward Only Surviving Read Percent: 14.19
Reverse Only Surviving Reads: 378
Reverse Only Surviving Read Percent: 0.47
Dropped Reads: 4243
Dropped Read Percent: 5.24
####
D5-A_S1
Input Read Pairs: 73400
Both Surviving Reads: 62641
Both Surviving Read Percent: 85.34
Forward Only Surviving Reads: 6434
Forward Only Surviving Read Percent: 8.77
Reverse Only Surviving Reads: 776
Reverse Only Surviving Read Percent: 1.06
Dropped Reads: 3549
Dropped Read Percent: 4.84
####
D6-B_S4
Input Read Pairs: 132689
Both Surviving Reads: 119920
Both Surviving Read Percent: 90.38
Forward Only Surviving Reads: 5169
Forward Only Surviving Read Percent: 3.90
Reverse Only Surviving Reads: 2490
Reverse Only Surviving Read Percent: 1.88
Dropped Reads: 5110
Dropped Read Percent: 3.85
####
T4-B_S93
Input Read Pairs: 93329
Both Surviving Reads: 83581
Both Surviving Read Percent: 89.56
Forward Only Surviving Reads: 4876
Forward Only Surviving Read Percent: 5.22
Reverse Only Surviving Reads: 1466
Reverse Only Surviving Read Percent: 1.57
Dropped Reads: 3406
Dropped Read Percent: 3.65
####
TO-MIX_S84
Input Read Pairs: 163273
Both Surviving Reads: 148478
Both Surviving Read Percent: 90.94
Forward Only Surviving Reads: 7440
Forward Only Surviving Read Percent: 4.56
Reverse Only Surviving Reads: 2373
Reverse Only Surviving Read Percent: 1.45
Dropped Reads: 4982
Dropped Read Percent: 3.05
####
TO-WT_S83
Input Read Pairs: 140141
Both Surviving Reads: 123516
Both Surviving Read Percent: 88.14
Forward Only Surviving Reads: 9281
Forward Only Surviving Read Percent: 6.62
Reverse Only Surviving Reads: 1941
Reverse Only Surviving Read Percent: 1.39
Dropped Reads: 5403
Dropped Read Percent: 3.86
####
Undetermined_S0
Input Read Pairs: 561019
Both Surviving Reads: 449928
Both Surviving Read Percent: 80.20
Forward Only Surviving Reads: 57607
Forward Only Surviving Read Percent: 10.27
Reverse Only Surviving Reads: 8268
Reverse Only Surviving Read Percent: 1.47
Dropped Reads: 45216
Dropped Read Percent: 8.06
####
phages/data/summary_trimm_R 0 → 100644
View file @ 0a8b3f0a
R1T1_S27
Input Read Pairs: 173454
Both Surviving Reads: 142874
Both Surviving Read Percent: 82.37
Forward Only Surviving Reads: 22563
Forward Only Surviving Read Percent: 13.01
Reverse Only Surviving Reads: 671
Reverse Only Surviving Read Percent: 0.39
Dropped Reads: 7346
Dropped Read Percent: 4.24
####
R1T2_S43
Input Read Pairs: 112766
Both Surviving Reads: 102719
Both Surviving Read Percent: 91.09
Forward Only Surviving Reads: 4485
Forward Only Surviving Read Percent: 3.98
Reverse Only Surviving Reads: 2215
Reverse Only Surviving Read Percent: 1.96
Dropped Reads: 3347
Dropped Read Percent: 2.97
####
R1T3_S59
Input Read Pairs: 66247
Both Surviving Reads: 54910
Both Surviving Read Percent: 82.89
Forward Only Surviving Reads: 8190
Forward Only Surviving Read Percent: 12.36
Reverse Only Surviving Reads: 453
Reverse Only Surviving Read Percent: 0.68
Dropped Reads: 2694
Dropped Read Percent: 4.07
####
R1T4_S75
Input Read Pairs: 173253
Both Surviving Reads: 137616
Both Surviving Read Percent: 79.43
Forward Only Surviving Reads: 27832
Forward Only Surviving Read Percent: 16.06
Reverse Only Surviving Reads: 595
Reverse Only Surviving Read Percent: 0.34
Dropped Reads: 7210
Dropped Read Percent: 4.16
####
R2T1_S28
Input Read Pairs: 213706
Both Surviving Reads: 176769
Both Surviving Read Percent: 82.72
Forward Only Surviving Reads: 21486
Forward Only Surviving Read Percent: 10.05
Reverse Only Surviving Reads: 4633
Reverse Only Surviving Read Percent: 2.17
Dropped Reads: 10818
Dropped Read Percent: 5.06
####
R2T2_S44
Input Read Pairs: 114571
Both Surviving Reads: 102263
Both Surviving Read Percent: 89.26
Forward Only Surviving Reads: 6792
Forward Only Surviving Read Percent: 5.93
Reverse Only Surviving Reads: 1439
Reverse Only Surviving Read Percent: 1.26
Dropped Reads: 4077
Dropped Read Percent: 3.56
####
R2T3_S60
Input Read Pairs: 147584
Both Surviving Reads: 130674
Both Surviving Read Percent: 88.54
Forward Only Surviving Reads: 10140
Forward Only Surviving Read Percent: 6.87
Reverse Only Surviving Reads: 1860
Reverse Only Surviving Read Percent: 1.26
Dropped Reads: 4910
Dropped Read Percent: 3.33
####
R2T4_S76
Input Read Pairs: 118585
Both Surviving Reads: 107616
Both Surviving Read Percent: 90.75
Forward Only Surviving Reads: 5267
Forward Only Surviving Read Percent: 4.44
Reverse Only Surviving Reads: 2147
Reverse Only Surviving Read Percent: 1.81
Dropped Reads: 3555
Dropped Read Percent: 3.00
####
R3T1_S29
Input Read Pairs: 206748
Both Surviving Reads: 185927
Both Surviving Read Percent: 89.93
Forward Only Surviving Reads: 10247
Forward Only Surviving Read Percent: 4.96
Reverse Only Surviving Reads: 3612
Reverse Only Surviving Read Percent: 1.75
Dropped Reads: 6962
Dropped Read Percent: 3.37
####
R3T2_S45
Input Read Pairs: 108555
Both Surviving Reads: 95397
Both Surviving Read Percent: 87.88
Forward Only Surviving Reads: 7542
Forward Only Surviving Read Percent: 6.95
Reverse Only Surviving Reads: 1469
Reverse Only Surviving Read Percent: 1.35
Dropped Reads: 4147
Dropped Read Percent: 3.82
####
R3T3_S61
Input Read Pairs: 189599
Both Surviving Reads: 163023
Both Surviving Read Percent: 85.98
Forward Only Surviving Reads: 13976
Forward Only Surviving Read Percent: 7.37
Reverse Only Surviving Reads: 4831
Reverse Only Surviving Read Percent: 2.55
Dropped Reads: 7769
Dropped Read Percent: 4.10
####
R3T4_S77
Input Read Pairs: 123278
Both Surviving Reads: 109312
Both Surviving Read Percent: 88.67
Forward Only Surviving Reads: 6699
Forward Only Surviving Read Percent: 5.43
Reverse Only Surviving Reads: 2820
Reverse Only Surviving Read Percent: 2.29
Dropped Reads: 4447
Dropped Read Percent: 3.61
####
R4T1_S30
Input Read Pairs: 152971
Both Surviving Reads: 138017
Both Surviving Read Percent: 90.22
Forward Only Surviving Reads: 7580
Forward Only Surviving Read Percent: 4.96
Reverse Only Surviving Reads: 2184
Reverse Only Surviving Read Percent: 1.43
Dropped Reads: 5190
Dropped Read Percent: 3.39
####
R4T2-B_S88
Input Read Pairs: 2904
Both Surviving Reads: 2620
Both Surviving Read Percent: 90.22
Forward Only Surviving Reads: 118
Forward Only Surviving Read Percent: 4.06
Reverse Only Surviving Reads: 70
Reverse Only Surviving Read Percent: 2.41
Dropped Reads: 96
Dropped Read Percent: 3.31
####
R4T2_S46
Input Read Pairs: 173500
Both Surviving Reads: 151060
Both Surviving Read Percent: 87.07
Forward Only Surviving Reads: 14434
Forward Only Surviving Read Percent: 8.32
Reverse Only Surviving Reads: 1459
Reverse Only Surviving Read Percent: 0.84
Dropped Reads: 6547
Dropped Read Percent: 3.77
####
R4T3_S62
Input Read Pairs: 125155
Both Surviving Reads: 111315
Both Surviving Read Percent: 88.94
Forward Only Surviving Reads: 7708
Forward Only Surviving Read Percent: 6.16
Reverse Only Surviving Reads: 1856
Reverse Only Surviving Read Percent: 1.48
Dropped Reads: 4276
Dropped Read Percent: 3.42
####
R4T4_S78
Input Read Pairs: 135493
Both Surviving Reads: 119251
Both Surviving Read Percent: 88.01
Forward Only Surviving Reads: 9245
Forward Only Surviving Read Percent: 6.82
Reverse Only Surviving Reads: 1920
Reverse Only Surviving Read Percent: 1.42
Dropped Reads: 5077
Dropped Read Percent: 3.75
####
R5T1_S31
Input Read Pairs: 195155
Both Surviving Reads: 178171
Both Surviving Read Percent: 91.30
Forward Only Surviving Reads: 7689
Forward Only Surviving Read Percent: 3.94
Reverse Only Surviving Reads: 3631
Reverse Only Surviving Read Percent: 1.86
Dropped Reads: 5664
Dropped Read Percent: 2.90
####
R5T2_S47
Input Read Pairs: 76322
Both Surviving Reads: 65988
Both Surviving Read Percent: 86.46
Forward Only Surviving Reads: 6485
Forward Only Surviving Read Percent: 8.50
Reverse Only Surviving Reads: 830
Reverse Only Surviving Read Percent: 1.09
Dropped Reads: 3019
Dropped Read Percent: 3.96
####
R5T3_S63
Input Read Pairs: 145477
Both Surviving Reads: 111219
Both Surviving Read Percent: 76.45
Forward Only Surviving Reads: 26944
Forward Only Surviving Read Percent: 18.52
Reverse Only Surviving Reads: 532
Reverse Only Surviving Read Percent: 0.37
Dropped Reads: 6782
Dropped Read Percent: 4.66
####
R5T4_S79
Input Read Pairs: 351448
Both Surviving Reads: 318608
Both Surviving Read Percent: 90.66
Forward Only Surviving Reads: 16133
Forward Only Surviving Read Percent: 4.59
Reverse Only Surviving Reads: 6282
Reverse Only Surviving Read Percent: 1.79
Dropped Reads: 10425
Dropped Read Percent: 2.97
####
R6T1_S32
Input Read Pairs: 165216
Both Surviving Reads: 146223
Both Surviving Read Percent: 88.50
Forward Only Surviving Reads: 11260
Forward Only Surviving Read Percent: 6.82
Reverse Only Surviving Reads: 1605
Reverse Only Surviving Read Percent: 0.97
Dropped Reads: 6128
Dropped Read Percent: 3.71
####
R6T2_S48
Input Read Pairs: 156958
Both Surviving Reads: 140818
Both Surviving Read Percent: 89.72
Forward Only Surviving Reads: 8884
Forward Only Surviving Read Percent: 5.66
Reverse Only Surviving Reads: 2168
Reverse Only Surviving Read Percent: 1.38
Dropped Reads: 5088
Dropped Read Percent: 3.24
####
R6T3_S64
Input Read Pairs: 182061
Both Surviving Reads: 166771
Both Surviving Read Percent: 91.60
Forward Only Surviving Reads: 5671
Forward Only Surviving Read Percent: 3.11
Reverse Only Surviving Reads: 4912
Reverse Only Surviving Read Percent: 2.70
Dropped Reads: 4707
Dropped Read Percent: 2.59
####
R6T4_S80
Input Read Pairs: 162599
Both Surviving Reads: 144168
Both Surviving Read Percent: 88.66
Forward Only Surviving Reads: 11225
Forward Only Surviving Read Percent: 6.90
Reverse Only Surviving Reads: 1755
Reverse Only Surviving Read Percent: 1.08
Dropped Reads: 5451
Dropped Read Percent: 3.35
####
R7R1_S33
Input Read Pairs: 84379
Both Surviving Reads: 71829
Both Surviving Read Percent: 85.13
Forward Only Surviving Reads: 7378
Forward Only Surviving Read Percent: 8.74
Reverse Only Surviving Reads: 1103
Reverse Only Surviving Read Percent: 1.31
Dropped Reads: 4069
Dropped Read Percent: 4.82
####
R7R2_S49