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
A9 F1 I0 R1 47 168.9 3047894 98.0% 2986936 264.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC NC_000913 3,992,523 (CGGGC)2→1 2.5% coding (1372‑1376/2547 nt) cyaA → adenylate cyclase

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 3992521 =274 (1.690)7 (0.040) 7/492 NT 2.5% coding (1370/2547 nt) cyaA adenylate cyclase
?NC_000913 = 3992515 269 (1.700)coding (1364/2547 nt) cyaA adenylate cyclase

ATCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3992812‑3992521
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcccggcGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCACGCACCTGATCAATCTTCCAGTTAGCGCGGTTATCGAGCATTGCCAGACGAGCTTCGTCCC  <  NC_000913/3992515‑3992230
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
ATCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCC                                                                                                                                                                                                                                                                                                    >  2:723611/1‑289
ATCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCC                                                                                                                                                                                                                                                                                                    >  2:27576/1‑289
ATCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCC                                                                                                                                                                                                                                                                                                    >  2:183721/1‑289
 TCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCG                                                                                                                                                                                                                                                                                                   >  1:936858/1‑289
                          GCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCGGCACATAAATAAAGGT‑CAGAT                                                                                                                                                                                                                                                                          <  2:673581/288‑1
                                               CGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCCTCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGATTCAATATTTGGCGCGCGGTTATTAAGATACCAACCTGAACGGTTAGCTCGGCGGCACATAAATAAAGGT‑AAGATTAGGTTCCGAGAGAACGGGGGA                                                                                                                                                                                                                                                    >  1:1440404/1‑289
                                                                                                                  TCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCGGCACATACATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTC                                                                                                                                                                                 >  2:1168252/1‑289
                                                                                                                                                    TGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGA                                                                                                                                                    <  1:468672/284‑1
                                                                                                                                                    TGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGA                                                                                                                                                    >  2:468672/1‑284
                                                                                                                                                                                TGCCCACACCACCAGTGTATTCAGGGAACGTTGTTATTCCATCGGCGGAGTGCTGGGGATCGACTCAATATGCGGCGCTCGGTTATACAGATACCAACCTTAACGTTTAGCCCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCGGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACCCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGAT                                                                                                                   <  1:1168252/289‑1
                                                                                                                                                                                                                                     TGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCA                                                               <  2:1440404/288‑1
                                                                                                                                                                                                                                                                                             GCCCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCG                                                                    <  1:721385/227‑1
                                                                                                                                                                                                                                                                                             GCCCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCG                                                                    >  2:721385/1‑227
                                                                                                                                                                                                                                                                                             GCCCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATATGCGGGTTTACCAGCGTCACTTTACCTGGTCATGCTTCAACCGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTTCGAAGCGCAACGCGGATCAGGTTACCGCAGATCTGCATCATCGCGTCGAACAACCCGTTGTGCGCCCCACCCCCCTTCTCACTCTTTACGTTAGCGCGGTCATCGGACACTTGCAGACGAGCTTC       >  1:730904/1‑288
                                                                                                                                                                                                                                                                                               CCGGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCACGCACCTGATCAATCTTCCAGTTAGCGCGGTTATCGAGCATTGCCAGACGAGCTTCGT     >  1:455066/1‑288
                                                                                                                                                                                                                                                                                                CGGCGGCACATAAA‑AAAGGTGCAAATTCGGTTCCGAGAGATCGGTTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAACCGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCACGCACCTGATCAATCTTCCAGTTAGCGCGGTTATCGAGCATTGCCAGACGAGCTTCGTCC   <  1:1357821/289‑1
                                                                                                                                                                                                                                                                                                 GGCGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCACGCACCTGATCAATCTTCCAGTTAGCGCGGTTATCGAGCATTGCCAGACGAGCTTCGTCCC  <  2:1452494/289‑1
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
ATCGCCAGATGGCGGATCTCACACGGGCTGTAGAGCGCCTTCGGTGTCGGTGCAGGTAAGCGCAGCGGGAAATGGTGCGACACGTCGGCGACCATCTCCTGCAACTTAGGCAAATCGACAATGCCGTTACCTTTAATATACAAACGGGTGCGCGAGGTCAGCAGGCCGTTAAACCATGCCCACGCCACCAGTTTATTCAGGTAACGGTTATATTCCAGCGGCTGATGGCTGATGATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3992812‑3992521
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcccggcGGCACATAAATAAAGGT‑CAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTTACCTGGTAATGCTTCAAACGCGGCATACAGCTTACGCGTCAGCACGCCGATATCCTGCGGACTGGCGGAGACGCTAAGGTTATTGCGACGCGCAAAGCGGATCAGATTACGGTAGCTCTGCATCATCGCGTCGAGCAACTCGTTGTGCGCCTCACGCACCTGATCAATCTTCCAGTTAGCGCGGTTATCGAGCATTGCCAGACGAGCTTCGTCCC  <  NC_000913/3992515‑3992230

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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