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 F13 I0 R1 213 60.4 2554362 98.6% 2518600 147.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC NC_002947_CJ‑RC 1,780,067 Δ62 bp 63.7% intergenic (+26/+19) PP_1587 → / ← dapC NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC = 17800663 (0.050)6 (0.110) 6/258 NT 63.7% intergenic (+25/+81) PP_1587/dapC NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase
?NC_002947_CJ‑RC 1780129 = 4 (0.080)intergenic (+88/+18) PP_1587/dapC NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase

CAACCTGCATCGTCAGCACCTGGTGGGGGATGAGGTGGTGCGGCAAGTACTGGGTGAGCTGGATATGAGTGAGGCGAACCTGGGTTCAGTCAAGTAGACCCTATCAAGGCCCTTCGCGGGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947_CJ‑RC/1779945‑1780066
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcgggcgTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTTCACCCCATCCACTTCACGCGACAGGTACGAC  >  NC_002947_CJ‑RC/1780129‑1780276
                                                                                                                                                                                                                                                                              
CAACCTGCATCGTCAGCACCTGGTGGGGGATGAGGTGGTGCGGCAAGTACTGGGTGAGCTGGATATGAGTGAGGCGAACCTGGGTTCAGTCAAGTAGACCCTATCAAGGCCCTTCGCGGGCGTGCCCGCGAAGGGGTTGATCAGCGGTT                                                                                                                           <  8:276591/149‑1
                                  GTGGTGCGGCAAGTACTGGGTGAGCTGGATATGAGTGAGGCGAACCTGGGTTCAGTCAAGTAGACCCTATCAAGGCCCTTCGCGGGCGTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTC                                                                                          >  1:227280/1‑148
                                                           TGGATATGAGTGAGGCGAACCTGGGTTCAGTCAAGTAGACCCTATCAAGGCCCTTCGCGGGCGTGCCCGCCAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGGGAATGCGCTCCGCCGCTTAGATGGATTCGGCCAGCGGGGCAACCc                                                                >  4:34123/1‑148
                                                                                           AAGTAGACCCTATCAAGGCCCTTCGCGGGCGTGCCCGCGAAGGGGTTGTTCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTT                                 <  2:227280/148‑1
                                                                                                          AGGCCCTTCGCGGGCGTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTTCACCCCATC                        >  5:302181/1‑142
                                                                                                          AGGCCCTTCGCGGGCGTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTTCACCCCATC                        <  6:302181/142‑1
                                                                                                               CTTCGCGGGCGTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTT                                 >  5:247893/1‑128
                                                                                                               CTTCGCGGGCGTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTT                                 <  6:247893/128‑1
                                                                                                                       GCGTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTTCACCCCATCCACTTCACGCGACAGGTAC     >  6:242228/1‑148
                                                                                                                         GTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTTCACCCCATCCACTTCACGCGACAGGTACGAC  >  7:222987/1‑149
                                                                                                                                                                                                                                                                              
CAACCTGCATCGTCAGCACCTGGTGGGGGATGAGGTGGTGCGGCAAGTACTGGGTGAGCTGGATATGAGTGAGGCGAACCTGGGTTCAGTCAAGTAGACCCTATCAAGGCCCTTCGCGGGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947_CJ‑RC/1779945‑1780066
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcgggcgTGCCCGCGAAGGGGTTGATCAGCGGTTTTGCAGGAAGGCGCGAATGCGCTCCGCCGCTTCGATGCATTCGGCCAGCGGTGCAACCAGTGCCATGCGCACGCGCCCGGCACCCGGGTTCACCCCATCCACTTCACGCGACAGGTACGAC  >  NC_002947_CJ‑RC/1780129‑1780276

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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