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
A14 F3 I1 R1 17 29.0 1011270 93.1% 941492 143.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 4,111,596 G→A L179L (CTG→TTG)  yiiQ ← DUF1454 family putative periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA4,111,5960GA100.0% 45.8 / NA 18L179L (CTG→TTG) yiiQDUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/8);  total (10/8)

AAAGGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAAT  >  NC_000913_3_pae_tpiA/4111451‑4111723
                                                                                                                                                  |                                                                                                                               
aaaTGAATATGGCCGCCCCCGAGGGCAGCAGGTCTGTGAAACAGTAGAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTCCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAAccc                                                                                                                              <  1:398120/149‑1 (MQ=255)
    gAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCttt                                                                                                                          >  1:351565/1‑149 (MQ=255)
            ccgccCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCTCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGtt                                                                                                                  <  1:80552/149‑1 (MQ=255)
            ccgccCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGtt                                                                                                                  >  1:298532/1‑149 (MQ=255)
                cccGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTcc                                                                                                              <  1:24070/149‑1 (MQ=255)
                          agcagGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACAt                                                                                                    >  1:192108/1‑149 (MQ=255)
                                   gtgAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCATTg                                                                                           >  1:212927/1‑149 (MQ=255)
                                              taGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGCTTCAGATAGCGCCAGCTTAATCGATT‑AACACGCCACGGTTAACCCCGTTTTGCCGTTGTCCGCGCCAACATAACGCAGAGCACCTTCTGtt                                                                                >  2:156074/1‑148 (MQ=255)
                                                   aTTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCGCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGgt                                                                           >  2:407979/1‑149 (MQ=255)
                                                   aTTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGgt                                                                           >  1:95707/1‑149 (MQ=255)
                                                                   gctttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACgtttgttt                                                           <  2:95707/149‑1 (MQ=255)
                                                                       tgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTcc                                                       <  2:192108/149‑1 (MQ=255)
                                                                                acATTAATTCAAACCTTCAAACCATTCAGATAGCGCCAGTTTAATCGGTTCAACA‑GCGAAGGTCAACCCTTTTTCGCCGTTGCCCGCGACAACATAACGCAGTGCACCCTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTta                                              <  2:363987/148‑1 (MQ=255)
                                                                                           aaCCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTCATCAGGTTTGGTTTTCCCCGCCGTTAGTAGCGACTGc                                   >  2:358307/1‑149 (MQ=255)
                                                                                                   aGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GAGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACCACATAACGACGAGCACATTCTATATCGCACTAAAACCGTTTGTTTTTCCCCGCCGATATTAGTGATGGCAGtatttt                           >  2:142283/1‑149 (MQ=255)
                                                                                                      gATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTg                        >  1:110929/1‑149 (MQ=255)
                                                                                                                    cAGCTTAATCGGTTCAACA‑GCGAAGGTCAACCCCTTTGCGCCGTTGTCCGCAACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTgg          <  2:287270/149‑1 (MQ=255)
                                                                                                                            tCGGTTCAACA‑GCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAAt  <  2:110929/149‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                               
AAAGGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACA‑GCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAAT  >  NC_000913_3_pae_tpiA/4111451‑4111723

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A