Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F17 I0 R1 49 108.0 2318666 92.3% 2140128 226.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC NC_000913 2,536,312 Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp 7.0% coding (479‑484/510 nt) crr → glucose‑specific enzyme IIA component of PTS

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 2514274 =NA (NA)3 (0.030) 3/424 NT 3.8% noncoding (2/1345 nt) IS186 repeat region
?NC_000913 = 2536317 73 (0.770)coding (484/510 nt) crr glucose‑specific enzyme IIA component of PTS
Rejected: Frequency below/above cutoff threshold.
* ? NC_000913 = 2515616NA (NA)8 (0.080) 7/426 NT 9.6% noncoding (1344/1345 nt) IS186 repeat region
?NC_000913 2536312 = 73 (0.770)coding (479/510 nt) crr glucose‑specific enzyme IIA component of PTS

AGCAGAGTTGCAGCATCACGAATTTCGCGGCGGCGGGTTAGAGCCCCGGCATTACGTGCCGAAGTATCCAGTTCTTCGGGCTTACCAATATGGGCCAGAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2514461‑2514274
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggTTTCACCCACGGTTACGCTACCGGACAGTTTGATCAGTTCTTTGATTTCGTCCATGTTGGAGATAACAACCGGAGTCAGGGTAGACTTGGCTTTCTCTTCCAGCAGCGGCAGATCAAATTCAATGACAGTATCGCCAACTTTCACGCGCTGACCTTCTTCAGCAATACGCTTGAAGCCTTCGCCTTTCAGTTCAACGGTGTCGATACCGAAGTGGACGAACAGTTCAACGCCGCTA  <  NC_000913/2536317‑2536082
                                                                                                                                                                                                                                                                                                                                                                                                                                        
AGCAGAGTTGCAGCATCACGAATTTCGCGGCGGCGGGTTAGAGCCCCGGCATTACGTGCCGAAGTATCCAGTTCTTCGGGCTTACCAATATGGGCCAGAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTTCACCCACGGTTACGCTACCGGACAGTTTGATCAGTTCTTTGATTTCG                                                                                                                                                                                            >  1:23041/1‑238
               TCACGAATTTCGCGGCGGCGGGTTAGAGCCCCGGCATTACGTGCCGAAGTATCCAGTTCTTCGGGCTTACCAATATGGGCCAGAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTTCACCCACGGTTACGCTACCGGACAGTTTGATCAGTTCTTTGATTTCGTCCATGTTGGAGATA                                                                                                                                                                             >  1:361165/1‑238
                         CGCGGCGGCGGGTTAGAGCCCCGGCATTACGTGCCGAAGTATCCAGTTCTTCGGGCTTACCAATATGGGCCAGAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTTCACCCACGGTTACGCTACCGGACAGTTTGATCAGTTCTTTGATTTCGTCCATGTTGGAGATAACAACCGGAGT                                                                                                                                                                  <  1:383461/239‑1
                                                                                                                                                                                          GGTTTCACCCACGGTTACGCTACCGGACAGTTTGATCAGTTCTTTGATTTCGTCCATGTTGGAGATAACAACCGGAGTCAGGGTAGACTTGGCTTTCTCTTCCAGCAGCGGCAGATCAAATTCAATGACAGTATCGCCAACTTTCACGCGCTGACCTTCTTCAGCAATACGCTTGAAGCCTTCGCCTTTCAGTTCAACGGTGTCGATACCGAAGTGGACGAACAGTTCAACGCCGCTA  <  1:533041/238‑1
                                                                                                                                                                                                                                                                                                                                                                                                                                        
AGCAGAGTTGCAGCATCACGAATTTCGCGGCGGCGGGTTAGAGCCCCGGCATTACGTGCCGAAGTATCCAGTTCTTCGGGCTTACCAATATGGGCCAGAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2514461‑2514274
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggTTTCACCCACGGTTACGCTACCGGACAGTTTGATCAGTTCTTTGATTTCGTCCATGTTGGAGATAACAACCGGAGTCAGGGTAGACTTGGCTTTCTCTTCCAGCAGCGGCAGATCAAATTCAATGACAGTATCGCCAACTTTCACGCGCTGACCTTCTTCAGCAATACGCTTGAAGCCTTCGCCTTTCAGTTCAACGGTGTCGATACCGAAGTGGACGAACAGTTCAACGCCGCTA  <  NC_000913/2536317‑2536082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A