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
A13 F1 I2 R1 762 35.5 1545288 95.5% 1475750 117.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,054,439 A→G T280T (ACT→ACC)  glnG ← fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,054,4390AG100.0% 65.1 / NA 20T280T (ACT→ACC) glnGfused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (11/9);  total (11/9)

CAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGAGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTTCGTCG  >  NC_000913/4054316‑4054565
                                                                                                                           |                                                                                                                              
cAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATc                                                                                                                 <  2:305360/139‑1 (MQ=255)
  gACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCTGATAACGGTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCg                                                                                                               <  2:208622/139‑1 (MQ=255)
                 cccGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCAc                                                                                                <  2:246316/139‑1 (MQ=255)
                               aGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTATTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACAACCACTCTCACCGGCGCATAgccgc                                                                                  >  2:408265/1‑139 (MQ=255)
                                                  ggATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCTAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGAcc                                                               <  2:489188/139‑1 (MQ=255)
                                                    aTAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGt                                                             >  2:114963/1‑139 (MQ=255)
                                                              ggCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCAc                                                   >  1:734215/1‑139 (MQ=255)
                                                              ggCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCAc                                                   >  2:40502/1‑139 (MQ=255)
                                                               gCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCAcg                                                  >  1:91358/1‑139 (MQ=255)
                                                                             ccTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGt                                    >  1:673776/1‑139 (MQ=255)
                                                                               tCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCt                                  >  2:704991/1‑139 (MQ=255)
                                                                                    gAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGcaca                             <  1:106448/139‑1 (MQ=255)
                                                                                               ccTGCACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCat                  <  1:653642/139‑1 (MQ=255)
                                                                                                   cACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAAcgc                                      >  1:266549/1‑115 (MQ=255)
                                                                                                   cACTCGCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAAcgc                                      <  2:266549/115‑1 (MQ=255)
                                                                                                        gCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAAt         >  2:207906/1‑139 (MQ=255)
                                                                                                        gCTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAAt         >  1:345158/1‑139 (MQ=255)
                                                                                                         cTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAAcg                                       <  1:544311/108‑1 (MQ=255)
                                                                                                         cTGTTCGAGATTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAAcg                                       >  2:544311/1‑108 (MQ=255)
                                                                                                               gagaTTCTGGTGGGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTtcgtcg  <  1:144301/139‑1 (MQ=255)
                                                                                                                           |                                                                                                                              
CAGACGGGGAATATCTTCCCGACGTTCGCGCAGCGGCGGCAGATGAACGCGGATAACGTTCAGGCGGTGGAACAGATCCTCACGGAACTTACCTTCCTGCACTCGCTGTTCGAGATTCTGGTGAGTGGCAGCGATAATCCGCACATCCACTTTCACCGGCGCATAGCCGCCAACGCGGTAAAACTGACCGTCTGCCAGCACGCGCAGCAAACGCGTCTGCACATCCAGCGGCATATCACCAATTTCGTCG  >  NC_000913/4054316‑4054565

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