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
A1 F28 I1 R1 163 52.9 1786516 99.3% 1774010 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,216,955 T→C G59G (GGT→GGC)  nfeR → DNA‑binding transcriptional repressor NfeR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,216,9550TC100.0% 128.6 / NA 38G59G (GGT→GGC) nfeRDNA‑binding transcriptional repressor NfeR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/20);  total (18/20)

GCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGTCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTACACCCCAAGCCCGGGCGTCATCTACCC  >  NC_000913/3216820‑3217083
                                                                                                                                       |                                                                                                                                
gccaCGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACg                                                                                                                              >  1:115312/1‑140 (MQ=255)
gccaCGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACg                                                                                                                              <  1:797608/140‑1 (MQ=255)
gccaCGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACg                                                                                                                              >  2:570937/1‑140 (MQ=255)
               ctgctgCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTgg                                                                                                               >  2:302057/1‑140 (MQ=255)
               ctgctgCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTgg                                                                                                               <  2:278178/140‑1 (MQ=255)
                    gcAAAGGTGAGAAGTCAGAACGCGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTGCTTTGGCCACGGTGAATTACGTCTGGTGAtt                                                                                                          <  1:144780/140‑1 (MQ=255)
                       aaGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTg                                                                                                       >  1:868312/1‑140 (MQ=255)
                          gTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGGCTGGGGAGTCTGGat                                                                                                    >  2:564320/1‑140 (MQ=255)
                            gagaAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGatat                                                                                                  >  2:655355/1‑140 (MQ=255)
                             agaAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATAtt                                                                                                 >  1:69733/1‑140 (MQ=255)
                               aaGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATtct                                                                                               >  1:284526/1‑140 (MQ=255)
                                 gTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATtctct                                                                                             <  1:655355/140‑1 (MQ=255)
                                 gTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATtctct                                                                                             <  2:159990/140‑1 (MQ=255)
                                    aGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGCCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTcgc                                                                                          >  2:381320/1‑140 (MQ=255)
                                     gAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTcgcg                                                                                         <  2:126537/140‑1 (MQ=255)
                                           gAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGa                                                                                   >  2:211019/1‑140 (MQ=255)
                                               aCTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGc                                                                               <  2:868312/140‑1 (MQ=255)
                                                cTGCGGACACGGTCACCAGCAGGAACACTGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGcc                                                                              <  2:41364/140‑1 (MQ=255)
                                                 tGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCa                                                                             <  2:307707/140‑1 (MQ=255)
                                                  gCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATtctct                                                                                             <  1:249233/123‑1 (MQ=255)
                                                  gCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATtctct                                                                                             >  2:249233/1‑123 (MQ=255)
                                                     gACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGt                                                                         >  2:347759/1‑140 (MQ=255)
                                                        acGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCCGGCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTTTCGCGCGGTGCCAGCCACGGTTAc                                                                      >  2:432976/1‑140 (MQ=255)
                                                           gTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGaa                                                                   >  1:840649/1‑140 (MQ=255)
                                                                     tGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAg                                                         <  1:347759/140‑1 (MQ=255)
                                                                                 aTGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTg                                                   <  2:200431/134‑1 (MQ=255)
                                                                                 aTGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTg                                                   >  1:200431/1‑134 (MQ=255)
                                                                                         gtggtCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAg                                     <  2:69733/140‑1 (MQ=255)
                                                                                           ggtCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAggg                                   <  2:811649/140‑1 (MQ=255)
                                                                                           ggtCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAggg                                   <  2:823959/140‑1 (MQ=255)
                                                                                            gtCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAgggg                                  >  1:542/1‑140 (MQ=255)
                                                                                               gCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAAccc                                       <  2:209310/132‑1 (MQ=255)
                                                                                               gCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAAccc                                       >  1:209310/1‑132 (MQ=255)
                                                                                                 cACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTa                             <  2:329707/140‑1 (MQ=255)
                                                                                                 cACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTa                             <  2:115312/140‑1 (MQ=255)
                                                                                                      tCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTACAccc                        >  1:118273/1‑140 (MQ=255)
                                                                                                         cggcggcggTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTACACCCCaa                     >  2:237160/1‑140 (MQ=255)
                                                                                                            cggcggTCGTCGGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTACACCCCAAGcc                  <  2:761651/140‑1 (MQ=255)
                                                                                                                      cgGCAACGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTACACCCCAAGCCCGGGCGTCAt        <  2:234709/140‑1 (MQ=255)
                                                                                                                            cGTTTCTTTGGCCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTACACCCCAAGCCCGGGCGTCATCTAccc  >  2:130886/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                
GCCACGCCATGAGGGCTGCTGCAAAGGTGAGAAGTCAGAACACGAGCACTGCGGACACGGTCACCAGCATGAACACGGTCAATGCTGCGGTGGTCGCCACGGTCGCGGCGGCGGTCGTCGGCAACGTTTCTTTGGTCACGGTGAATTACGTCTGGTGATTCTGGATATTCTCTCGCGCGATGACAGCCACGGTTACGAATTGATTAAAGCGATTGAGAATCTAACCCAGGGGAATTACACCCCAAGCCCGGGCGTCATCTACCC  >  NC_000913/3216820‑3217083

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A