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
A5 F28 I1 R2 164 48.3 4710601 85.3% 4018142 55.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 1,303,631 C→T Q246Y (CAG→TAT)  oppA → oligopeptide transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,303,6310CT100.0% 140.0 / NA 43Q246Y (CAG→TAT) oppAoligopeptide transporter subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/24);  total (19/24)

TCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCT  >  W3110S.gb/1303582‑1303679
                                                 |                                                
tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                      >  1:3622758/1‑62 (MQ=255)
tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                      >  1:1115940/1‑62 (MQ=255)
tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                      >  1:2977009/1‑62 (MQ=255)
tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                      >  1:153789/1‑62 (MQ=255)
tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                      >  1:4338440/1‑62 (MQ=255)
tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                      >  1:561765/1‑62 (MQ=255)
 cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTaa                                            <  1:2076405/55‑1 (MQ=255)
 cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTaa                                            <  1:4157045/55‑1 (MQ=255)
 cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTaa                                            <  1:4208019/55‑1 (MQ=255)
 cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTaa                                            <  1:281111/55‑1 (MQ=255)
 cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTaa                                            <  1:1843308/55‑1 (MQ=255)
 cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAttt                                     >  1:3779411/1‑62 (MQ=255)
 cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAttt                                     >  1:2475601/1‑62 (MQ=255)
      aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGc                                   <  1:871350/59‑1 (MQ=255)
      aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGc                                   <  1:2951137/59‑1 (MQ=255)
        gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAtt                              <  1:3699511/62‑1 (MQ=255)
        gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAtt                              <  1:4585842/62‑1 (MQ=255)
        gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAtt                              <  1:2187678/62‑1 (MQ=255)
        gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAtt                              <  1:4451472/62‑1 (MQ=255)
          aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                            <  1:690609/62‑1 (MQ=255)
          aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                            <  1:69808/62‑1 (MQ=255)
          aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                            <  1:1193792/62‑1 (MQ=255)
          aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                            <  1:1396946/62‑1 (MQ=255)
          aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                            <  1:1473387/62‑1 (MQ=255)
          aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                            <  1:1665015/62‑1 (MQ=255)
          aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                            <  1:1936278/62‑1 (MQ=255)
                aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                      <  1:1019371/62‑1 (MQ=255)
                aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                      <  1:620212/62‑1 (MQ=255)
                aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                      <  1:3423186/62‑1 (MQ=255)
                aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                      <  1:1591824/62‑1 (MQ=255)
                aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                      <  1:1013596/62‑1 (MQ=255)
                     cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa                 >  1:35483/1‑62 (MQ=255)
                     cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa                 >  1:2848216/1‑62 (MQ=255)
                        gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGc                                   <  1:4677632/41‑1 (MQ=38)
                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa             >  1:52636/1‑62 (MQ=255)
                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa             >  1:1024978/1‑62 (MQ=255)
                            aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg           >  1:3044370/1‑61 (MQ=255)
                            aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg           >  1:2771090/1‑61 (MQ=255)
                            aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg           >  1:4422490/1‑61 (MQ=255)
                            aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg           >  1:2152791/1‑61 (MQ=255)
                            aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg           >  1:1644759/1‑61 (MQ=255)
                                    aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCt  >  1:254234/1‑62 (MQ=255)
                                    aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCt  >  1:1592548/1‑62 (MQ=255)
                                                 |                                                
TCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCT  >  W3110S.gb/1303582‑1303679

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A