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
A23 F999 I0 R1 108 31.0 2704742 83.3% 2253050 49.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,720,597 Δ1 bp coding (4/153 nt) hokA ← small toxic polypeptide

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,720,5960G.100.0% 177.2 / NA 37coding (5/153 nt)hokAsmall toxic polypeptide
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (12/25);  total (12/25)

TAAAAGCGTGAAACAAATCACTATTAAAGAAAGTAATCTATATTTCTGCGGCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATGTACTGCA  >  NC_000913/3720547‑3720641
                                                 |                                             
tAAAAGCGTGAAACAAATCACTATTAAAGAAAGTAATCTATATTTCTGCg                                               >  1:813884/1‑50 (MQ=255)
  aaaGCGTGAAACAAATCACTATTAAAGAAAGTAATCTATATTTCTGCgca                                             >  1:719071/1‑48 (MQ=255)
       gTGAAACAAATCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTccc                                       <  1:2529522/50‑1 (MQ=255)
        tGAAACAAATCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCa                                      <  1:1753307/50‑1 (MQ=255)
            aCAAATCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGcct                                  <  1:1518525/50‑1 (MQ=255)
              aaaTCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGcctcc                                >  1:1615090/1‑50 (MQ=255)
              aaaTCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGcctcc                                >  1:172680/1‑50 (MQ=255)
              aaaTCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGcctcc                                <  1:1741720/50‑1 (MQ=255)
               aaTCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGcctcct                               <  1:624808/50‑1 (MQ=255)
                 tCACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGCCTCCtgt                             <  1:2435044/50‑1 (MQ=255)
                  cACTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGCCTCCtgtg                            >  1:2463831/1‑50 (MQ=255)
                   aCTATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTgtgt                           <  1:1512229/50‑1 (MQ=255)
                     tATTAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGtt                          >  1:333124/1‑49 (MQ=255)
                       ttAAAGAAAGTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTg                         <  1:2244311/48‑1 (MQ=255)
                       ttAAAGAAAGTAAACTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTg                         <  1:1166461/48‑1 (MQ=255)
                         aaagaaagTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGAtt                      <  1:2612094/49‑1 (MQ=255)
                          aagaaagTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTc                    >  1:1802538/1‑50 (MQ=255)
                          aagaaagTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTc                    <  1:1000288/50‑1 (MQ=255)
                           agaaagTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTcc                   <  1:1717994/50‑1 (MQ=255)
                           agaaagTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTcc                   <  1:2578791/50‑1 (MQ=255)
                              aagTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAAc                <  1:543358/50‑1 (MQ=255)
                              aagTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAAc                <  1:538237/50‑1 (MQ=255)
                               agTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACg               <  1:1768458/50‑1 (MQ=255)
                               agTAATCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACg               <  1:858539/50‑1 (MQ=255)
                                gTAATCTATATTTCTGC‑GCATTCCCAGCGTCCTGTGTTGATTTCCAAc                >  1:1703429/1‑48 (MQ=255)
                                   aTCTATATTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGt            <  1:1435899/49‑1 (MQ=255)
                                       atatTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaac       >  1:2700254‑M1/1‑47 (MQ=255)
                                       atatTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaac       >  1:414739‑M1/1‑47 (MQ=255)
                                        tatTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTAt          <  1:1854858/46‑1 (MQ=255)
                                        tatTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaact      <  1:966256‑M1/50‑5 (MQ=255)
                                        tatTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaact      >  1:1867749‑M1/1‑46 (MQ=255)
                                        tatTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaact      <  1:1299270‑M1/50‑5 (MQ=255)
                                        tatTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaa        <  1:1508812‑M1/48‑3 (MQ=255)
                                         atTTCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaactt     >  1:1615825‑M1/1‑45 (MQ=255)
                                          tttCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaacttt    >  1:2010788‑M1/1‑44 (MQ=255)
                                          tttCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaactt     <  1:397845‑M1/49‑6 (MQ=255)
                                            tCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaactttga  >  1:342087‑M1/1‑42 (MQ=255)
                                            tCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaactttg   <  1:2695457‑M1/49‑8 (MQ=255)
                                            tCTGC‑GCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATaactttg   <  1:2200624‑M1/49‑8 (MQ=255)
                                                 |                                             
TAAAAGCGTGAAACAAATCACTATTAAAGAAAGTAATCTATATTTCTGCGGCATTCCCAGCCTCCTGTGTTGATTTCCAACGAGTATGTACTGCA  >  NC_000913/3720547‑3720641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A