Mutation Analysis
v1
Inputs
Treated FASTQ
.fastq / .fq / .gz
(.fastq /.fq <500Mb, .gz <200Mb)
Control FASTQ
Optional for backgorund error filtering
(.fastq /.fq <500Mb, .gz <200Mb)
Protospacer (w/o PAM)
cacttcaatctggcccctct
e.g. GGCGCCCTGGCCAGTCGTCT
Additional Protospacer (w/o PAM, Optional)
ggcttagatatgacctgggt
Optional for second gRNA.
Reference
ctctcaaagcgctgggattagacacaagccaccacgcccagcctgtattttattttttaagggcgggcgccctcttctgttttataaaaggaacagtcgaattcctactggaagcgacgcgcgcagaggggaaggctttgtagacgccggctcgggtctggaatttaaagaactaaatttcgatgggtgaagacagtgggaaagggcggtggcatgatcctcgttttacagactaggaagtcgagcctcacgggagtgacggggcttctccgcaggctccgcgaagaaagcaaggctgggaggacccagacgaacggccacaacagcctcagcggccacgacagcctcagccgccaactcatgtcagccggcagagagtgcaggaagcgggcagctacagctccgctggggcgtggccttctgacgcaccgtcacggttccctctgtggccgcccattggctccctcttaccgcccttttccggggcaagggaagctagtagcggagccggaagtgaggcaccctcgggctcgagacagcggcgacgtttaaagctgagcgacccagtgccactggagacggtcagcttctccactcaggctcctccagcccgagccagaagaccccctcccccagaattctgggggccgatggaagggagccgagtcagatcgcgaggtacccagagccgacagaccggagcgacagggagttgccagaagccccgcccctaggagtgatcggaaagcctcacccatccgggtgaggaacccggagggaccgcctccgggcggagcccgccgaccatggctacgcccctggtggcgggtcccgcagctctacgcttcgccgccgcggctagctggcaggttgtgcgcggacgctgcgtggaacattttccgcgagtactggagtttctgcgatctctgcgcgctgttgcccctggcttggttcgctaccggcaccacgaacgcctttgtatgggcctaaaggccaaggtattggagcaagtaggacctggaaggggaaagaaagaaaggggcgggatgcgagcacctgacaagggcccacagcttggggatgagactagttggaaaaggtcagcttgccccgaagtggggattctgaattcagtaccgtacaggtggtggtggagctgatcctgcagggccggccttgggcccaagtcctgaaagccctgaatcaccactttccagaatctggacctatagtgcgggatcccaaggctgtgagtaatccccggaacaagccctgaccccagttacacttggtgcagcaaagttgctcctcctgtctactggatgttggtgctaacttctctgtcttctgtatcctcaacagacaaagcaggatctgaggaagattttggaggcacaggaaactttttaccagcaggtgaagcagctgtcagaggctcctgtggatttggcctcgaagctgcaggtgagactggtttgaaggctattatgtggctattttctctaacccatttttttttttttttgaggaatcttgctctgtcgcccaggctggagtgcagtggcacaatctcggctcactgcaacctctgcctcccgggttcaagcgattctcctgcctcagcctcccgagtagctgggattacaaatgcccagctaatttttgtattttagtagagatggggtttcaccatgttggccaggctggtctcgaactcctgacctcaagtgatccgcccacctcggcctcccaaatggccaggattacaggcgtgagccaccgtgcctggccactaacccacttttgacctaatctcccctgctgtaggaacttgaacaagagtatggggaaccctttctggctgccatggaaaagctgctttttgagtacttgtgtcagctggagaaagcactgcctacaccgcaggcacagcaggtttcgctggggcaaaacatgtaagggcagagtgtggggtggctgtttcaaggattgtggtcttcatacctctgtccctgcccacagcttcaggatgtgctgagttggatgcagcctggagtctctatcacctcttctcttgcctggagacaatatggtgtggacatggggtggctgcttccaggtactaggaatttggaggtgtagtgtttagcctgagaccttttgaggcagtccactggaatagttccatgggctccgggcataagaaaccagttattctgttactatctgttctctttataaggggcctcattttctttttcagagtgctctgttactgactcagtgaacctggctgagcccatggaacagaatcctcctcagcaacaaagactagcactccacaatcccctgccaaaagccaagcctggcacacatcttcctcagggaccatcttcaaggacgcacccagaacctctagctggccgacacttcaatctggcccctctaggccgacgaagagttcagtcccaatgggcctccactaggggaggccataaggagcgccccacagtcatgctgtttccctttaggaatctcggctcaccaacccaggtcatatctaagcctgagagcaaggaagaacatgcgatatacacagcagacctagccatgggcacaagagcagcctccactgggaagtctaagagtccatgccagaccctggggggaagggctctgaaggagaacccagttgacttgcctgccacagagcaaaaggagtgagtggaacagagttgcttcttactaggagcacattctttgcctgccttcccttcatcctatcctctttgcttgctctcacctcaggaattgcttggattgctacatggaccccctgagactatcattattacctcctagggccaggaagccaggtaggtagtctgagtcaggattggatcaacagcctcctctcttggggactctcaagagcctgtgttcatctagaagtagtagtttgattctggtttccctcctacagtgtgtcctccgtctctgtgcagctccgtcattaccataggggacttggttttagactctgatgaggaagaaaatggccagggggaaggaaaggtgagtgggaaggagcagaaagctgggaaaggggatgggtagaacaagactgagaaatccacatgcttcagaattcagagggttcagggaatggtttcggatagtaggctctccctgctcccttctctacaggaatctctggaaaactatcagaagacaaagtttgacaccttgatacccactctctgtgaatacctacccccttctggccacggtgccatacctgtttcttcctgtgactgtagagacagttctagacctttgtgatagaactaaaatgctctctgtactctagtctcctgcctcctcagctctgcaagtagtttagtaggaatgaagtggaagtccaggcttggattgcctaactacactgctaaaaatatttgtaatccttaataattaaactttggatttgttaaaatactgccttgatgtgaaggaggggaattaaggtttccataaggtcagcataagtcattccttagaaacagaactggcccttccaaactgaaaggatccctttgcctttttttacttcccttgctaagtgttgttcagctgtgcctaaaagggttagcagggttgaaagcctggaagagaaatgtcctttggtattctggaaatatgtgtcctcaggccagaatatactttgtaaattctcatgctgccagattatctgggtgtggtggcactagaatggagatacttcatgggaataatactcattgttcttgaccccactgggtcagtgctgaccctaccaccacccactctgcagcagcacccagatgctagccttgtacagaaagccccagcatctctttacagtcaatgagctctctctttattgaggtatttcaaatatacaaacacttcagagctttttagatatgtgaaggtccaatttagtgaagcggattaacaaaacatgattctaaaagcctgcctcctctagaccaaggccatgtaaaagatttatgtaccaatcagcatcttttccttttaataatcttcaggatgttgtgttgggtccccagattcccatttgattttcttgcatcattttctcagactgtttgcttccttgcttcctccccagtgagtgccttgggcattttgtgtgtgcagatagagaagtacagagttactgcaggagccctcaggagtgagacaacaggaaatgacaaagtaatacagagctgcagtagctgggatgggtgaggaccccacttgggatgccccatggtagagtactggtgccttgggagggtagaactgctcaggtctagcacgcctcactgaagattggattcacctgctgggtgactcggatgaaggtagttctcctgctcaactctttgagcttagctgctcccacataggtacacgtagagcggatccctcctaggatgtctcggatggtatgttccacatctcctttaaaaggaacttccactgtctttccctctgaggctcttaaagtaggaaaaactttattatcttctccttctggattccttaagcccagggacttttccacagaccctagcattgagccccggttcaccatgcttctctgagaactgtaccatccccctctcagcagccatgagttctgcctccatactattactaagctcctgggcctccacacatacctgtactcagccacgcccccagcatacttcttcatggccatttcagaactcattccatagaagagcttgtacttcttgccatccctctcgatgagctcaccacctgactcactgtgcccagccagcatgccacccagcatcacgaagtcagctcctgcccctgccaccatcatggaggggggaaagagattaatctggccaaggtgctcacatggccaccctcaaaagcaactcacaccatattctcagtcctgacaatgattccagcgtcttcctccttctgcttccctagctgacccacaatccacg
Note: For optimal performance, a reference sequence shorter than 25 kbp is recommended on web tool.
Intended edit (Optional)
Detailed options
Analysis window (nt)
Whole window between targets
True
False
Cleavage site in target (nt)
Large insertion length cutoff (nt)
Large deletion length cutoff (nt)
Examples
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FASTQ file alignment
Allele assignments
All pattern
WT vs other
Indel characterization
Combined
Insertions
Deletions
Large Deletions
Substitutions
Allele plot
