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 F1 I2 R1 730 35.1 2107516 91.4% 1926269 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,264,112 C→G A302A (GCG→GCC)  tdcC ← threonine/serine:H(+) symporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,264,1120CG100.0% 110.4 / NA 32A302A (GCG→GCC) tdcCthreonine/serine:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (12/20);  total (12/20)

AGATAGCCACGAGTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGA  >  NC_000913/3264036‑3264183
                                                                            |                                                                       
aGATAGCCACGGGTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCaa                                                                     <  1:610728/81‑1 (MQ=255)
  aTAGCCACGAGTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAg                                                                   >  2:610761/1‑81 (MQ=255)
     gCCACGAGTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTgg                                                                >  2:610776/1‑81 (MQ=255)
        aCGAGTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGt                                                               >  1:610779/1‑79 (MQ=255)
          gAGTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGc                                                           <  1:610729/81‑1 (MQ=255)
            gTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGc                                                           >  1:610785/1‑79 (MQ=255)
             tGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAg                                                        <  1:610730/81‑1 (MQ=255)
               cGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGAt                                                      <  1:610732/81‑1 (MQ=255)
               cGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGAt                                                      <  2:610731/81‑1 (MQ=255)
                 atgatgGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATaa                                                    <  1:610733/81‑1 (MQ=255)
                     tgGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGaaa                                                <  1:610734/81‑1 (MQ=255)
                     tgGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGa                                                  >  1:610791/1‑79 (MQ=255)
                      ggAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAg                                               >  1:610787/1‑81 (MQ=255)
                        aaGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCa                                             <  1:610735/81‑1 (MQ=255)
                          gCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACt                                           >  2:610774/1‑81 (MQ=255)
                            cGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTgg                                         <  2:610736/81‑1 (MQ=255)
                            cGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTgg                                         <  1:610737/81‑1 (MQ=255)
                                  ttCCAGTGTAATCGCGAACGTTGTTTTGGTATCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAatat                                    <  2:610738/80‑1 (MQ=255)
                                    ccAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTc                                  <  2:610739/80‑1 (MQ=255)
                                              cgcgAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGc                       >  1:610782/1‑81 (MQ=255)
                                               gcgAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCt                      <  2:610740/81‑1 (MQ=255)
                                                 gAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTc                    >  1:610781/1‑81 (MQ=255)
                                                 gAACGTTGTTTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTc                    >  1:610777/1‑81 (MQ=255)
                                                     gttgttTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGcc                <  2:610741/81‑1 (MQ=255)
                                                        gttTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCAt              <  2:610743/80‑1 (MQ=255)
                                                        gttTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCAt              <  1:610742/80‑1 (MQ=255)
                                                        gttTTGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATg             >  2:610795/1‑81 (MQ=255)
                                                         ttttGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATg             <  2:610744/80‑1 (MQ=255)
                                                            tGGTACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTg          <  2:610745/80‑1 (MQ=255)
                                                               tACCGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCg      <  2:610746/81‑1 (MQ=255)
                                                                 ccGGTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGga    <  2:610747/81‑1 (MQ=255)
                                                                   ggTCATGGAGGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGgaga  >  1:610786/1‑81 (MQ=255)
                                                                            |                                                                       
AGATAGCCACGAGTGCGATGATGGAAGCCGCATATTCCAGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGA  >  NC_000913/3264036‑3264183

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A