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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,808,741 T→C pseudogene (172/924 nt) ygaY → pseudogene, major facilitator transporter superfamily,putative transport, Not classified, putative transport protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,808,7410TC100.0% 186.1 / NA 53pseudogene (172/924 nt)ygaYpseudogene, major facilitator transporter superfamily,putative transport, Not classified, putative transport protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/26);  total (27/26)

GCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATG  >  NC_000913/2808606‑2808872
                                                                                                                                       |                                                                                                                                   
gCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTgg                                                                                                                                  <  2:149523/139‑1 (MQ=255)
        gatCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          >  1:277149/1‑139 (MQ=255)
                  aCGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:700395/139‑1 (MQ=255)
                  aCGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:519413/139‑1 (MQ=255)
                      cATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGt                                                                                                            >  1:400938/1‑139 (MQ=255)
                           aCCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCa                                                                                                                    >  2:311496/1‑126 (MQ=255)
                           aCCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCa                                                                                                                    <  1:311496/126‑1 (MQ=255)
                                         aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCt                                                                                                                        <  1:243783/108‑1 (MQ=255)
                                         aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCt                                                                                                                        >  2:243783/1‑108 (MQ=255)
                                         aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                >  2:726070/1‑116 (MQ=255)
                                         aGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:726070/116‑1 (MQ=255)
                                          gTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGt                                                                                                            <  2:1367617/119‑1 (MQ=255)
                                          gTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGt                                                                                                            >  1:1367617/1‑119 (MQ=255)
                                              tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          >  2:230560/1‑101 (MQ=255)
                                              tGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          <  1:230560/101‑1 (MQ=255)
                                                     aaTTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTgg                                                                             >  1:161406/1‑139 (MQ=255)
                                                         cTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCa                                                                         >  2:728505/1‑139 (MQ=255)
                                                               ccGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCt                                                                   >  1:510054/1‑139 (MQ=255)
                                                                      cAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTggga                                                            >  2:124379/1‑138 (MQ=255)
                                                                      cAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGt                                                            <  2:1063634/139‑1 (MQ=255)
                                                                      cAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGATCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGt                                                            <  1:373485/139‑1 (MQ=255)
                                                                         cGACGCTGACTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGc                                                         >  2:1257556/1‑139 (MQ=255)
                                                                           aCGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCtt                                                       <  1:728505/139‑1 (MQ=255)
                                                                            cGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTc                                                      <  2:277149/139‑1 (MQ=255)
                                                                             gCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCTGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCg                                                     <  1:124379/139‑1 (MQ=255)
                                                                               tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGa                                                                                                                               <  1:704424/63‑1 (MQ=255)
                                                                               tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGa                                                                                                                               >  2:704424/1‑63 (MQ=255)
                                                                               tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  1:544107/78‑1 (MQ=255)
                                                                               tGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                >  2:544107/1‑78 (MQ=255)
                                                                                   ttCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          >  1:883206/1‑64 (MQ=255)
                                                                                   ttCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTg                                                                                                                          <  2:883206/64‑1 (MQ=255)
                                                                                     cACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAAt                                             >  1:407784/1‑139 (MQ=255)
                                                                                      aCCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGcc                                                                                                        <  2:407063/79‑1 (MQ=255)
                                                                                      aCCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGcc                                                                                                        >  1:407063/1‑79 (MQ=255)
                                                                                           aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        >  2:439265/1‑106 (MQ=255)
                                                                                           aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        <  1:439265/106‑1 (MQ=255)
                                                                                           aTAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACt                                       >  1:1468162/1‑139 (MQ=255)
                                                                                            tAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTg                                      <  2:400938/139‑1 (MQ=255)
                                                                                               aCGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATg                                   >  2:1401507/1‑139 (MQ=255)
                                                                                                     cAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                <  2:1179563/56‑1 (MQ=255)
                                                                                                     cAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGa                                                                                                                >  1:1179563/1‑56 (MQ=255)
                                                                                                               ggCACTATTATGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGc                   <  1:1401507/139‑1 (MQ=255)
                                                                                                                    tattatGAGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGt              <  2:407784/139‑1 (MQ=255)
                                                                                                                           aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        >  1:916120/1‑74 (MQ=255)
                                                                                                                           aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGc                   >  2:1437398/1‑127 (MQ=255)
                                                                                                                           aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGc                   <  1:1437398/127‑1 (MQ=255)
                                                                                                                           aGCGGTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATCGCTGGCGAATCTCGGCGGCTGGCGCAc                                                                        <  2:916120/74‑1 (MQ=255)
                                                                                                                              ggTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                       >  1:795892/1‑72 (MQ=255)
                                                                                                                              ggTCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCAcc                                                                       <  2:795892/72‑1 (MQ=255)
                                                                                                                                tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCg                  <  2:817505/123‑1 (MQ=255)
                                                                                                                                tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGATTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCg                  >  1:817505/1‑123 (MQ=255)
                                                                                                                                tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGATGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTGTGGCGTGGTCTGCCACAAATg  >  2:164676/1‑139 (MQ=255)
                                                                                                                                tCTGCTGCTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTGTGGGTTGCTTCGGTGTTGATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATg  >  2:987749/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                                   
GCGATGATGATCCTCGGTACGGCATTAACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATG  >  NC_000913/2808606‑2808872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A