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 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,655,347 C→T *109* (TAG→TAA)  ynfA ← UPF0060 family inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,655,3470CT100.0% 186.3 / NA 58*109* (TAG→TAA) ynfAUPF0060 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (29/29);  total (29/29)

GATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGC  >  NC_000913/1655214‑1655463
                                                                                                                                     |                                                                                                                    
gATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGt                                                                                                                 <  1:18430/139‑1 (MQ=255)
   cGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTgcg                                                                                                              >  1:768835/1‑139 (MQ=255)
           gCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                      <  2:768835/139‑5 (MQ=255)
             cGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                   <  1:884161/139‑1 (MQ=255)
               gAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATTGATTTATGTTCTTACGTGCGccc                                                                                                           <  1:268929/130‑1 (MQ=255)
               gAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                           >  1:102005/1‑130 (MQ=255)
               gAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                           <  2:102005/130‑1 (MQ=255)
               gAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                           >  2:268929/1‑130 (MQ=255)
                aGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCTcaa                                                                                                >  2:1317775/1‑139 (MQ=255)
                aGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                <  1:1608675/139‑1 (MQ=255)
                                   gTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCa                                                                             >  1:275890/1‑139 (MQ=255)
                                                gtgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAAc                                                                >  2:281703/1‑139 (MQ=255)
                                                 tgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCa                                                                      <  2:972797/132‑1 (MQ=255)
                                                 tgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCa                                                                      >  1:972797/1‑132 (MQ=255)
                                                         tGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTGTGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                       <  2:1415289/139‑1 (MQ=255)
                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccag                                                                                                        >  1:523147/1‑87 (MQ=255)
                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccag                                                                                                        <  2:523147/89‑3 (MQ=255)
                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                       <  2:889102/137‑1 (MQ=255)
                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                       >  1:889102/1‑137 (MQ=255)
                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                     >  1:1392298/1‑139 (MQ=255)
                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                     >  1:1640135/1‑139 (MQ=255)
                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCATCCa                                                     <  2:275890/139‑1 (MQ=255)
                                                             aaaaGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACACACCCGTCCAGt                                                   <  2:379858/139‑1 (MQ=255)
                                                                           aaTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGt                                     >  1:340632/1‑139 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                         >  1:909978/1‑70 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                         <  2:909978/71‑2 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                   >  1:1361501/1‑76 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                   <  2:1361501/76‑1 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCAc                                                            >  2:358576/1‑115 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCAc                                                            <  1:358576/115‑1 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGtt                                    >  2:1685912/1‑139 (MQ=255)
                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGtt                                    <  2:1392298/139‑1 (MQ=255)
                                                                              aCCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTc                                  <  2:1640135/139‑1 (MQ=255)
                                                                                  tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                <  2:1628182/73‑1 (MQ=255)
                                                                                  tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                >  1:1628182/1‑73 (MQ=255)
                                                                                  tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCa                                                                             >  1:404024/1‑92 (MQ=255)
                                                                                  tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCa                                                                             <  2:404024/92‑1 (MQ=255)
                                                                                             acacTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGc                              <  2:1103128/128‑1 (MQ=255)
                                                                                             acacTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGc                              >  1:1103128/1‑128 (MQ=255)
                                                                                              cacTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgc                  <  2:1452497/139‑1 (MQ=255)
                                                                                                    ctctTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                         >  2:1472253/1‑46 (MQ=255)
                                                                                                    ctctTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                         <  1:1472253/47‑2 (MQ=255)
                                                                                                    ctctTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                       >  2:1826642/1‑96 (MQ=255)
                                                                                                    ctctTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                       <  1:1826642/96‑1 (MQ=255)
                                                                                                             tatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACg   >  2:450612/1‑139 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                         >  1:1083778/1‑36 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                         <  2:1083778/37‑2 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                           >  2:1591533/1‑35 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                           <  1:1591533/35‑1 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAGTGATCAACa                                                                                    >  1:1526732/1‑57 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACa                                                                                    <  2:1526732/57‑1 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                       <  1:1431172/86‑1 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                       >  2:1431172/1‑86 (MQ=255)
                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGc  >  2:961976/1‑139 (MQ=255)
                                                                                                               ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAgcg                                                                        >  2:813698/1‑68 (MQ=255)
                                                                                                               ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAgcg                                                                        <  1:813698/68‑1 (MQ=255)
                                                                                                               ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgcg                 >  2:388895/1‑123 (MQ=255)
                                                                                                               ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgcg                 <  1:388895/123‑1 (MQ=255)
                                                                                                                                     |                                                                                                                    
GATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGC  >  NC_000913/1655214‑1655463

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A