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
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,361,357	A→G	L193S (TTG→TCG)	cadC ←	cadBA operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,361,357	0	A	G	100.0%	118.0 / NA	32	L193S (TTG→TCG)	cadC	cadBA operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/18); total (14/18)

GGAGAAGGTGTTAAGTGATGTCGCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCAAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGAAAAAAAACCATACCCAAAAGGTAGTGAATCGTTTGCTTTTAACTGGGGA  >  NC_000913/4361230‑4361490

ggAGAAGGTGTTAAGTGCTGTCTCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGAt                                                                                                                            <  2:238167/139‑1 (MQ=255)

   gaAGGTGTTAAGTGATGTCGCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTg                                                                                                                         <  1:263801/139‑1 (MQ=255)

      ggTGTTAAGTGATGTCGCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTc                                                                                                                      <  1:160302/139‑1 (MQ=255)

               tGATGTCGCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGa                                                                                                             <  1:177364/139‑1 (MQ=255)

                 aTGTCGCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACg                                                                                                           >  2:417760/1‑139 (MQ=255)

                 aTGTCGCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACg                                                                                                           >  2:216455/1‑139 (MQ=255)

                       ccaccaAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATc                                                                                                     >  1:7731/1‑139 (MQ=255)

                                  cccACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGaaa                                                                                          <  2:2897/139‑1 (MQ=255)

                                         cTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTAc                                                                                   <  2:7731/139‑1 (MQ=255)

                                         cTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTAc                                                                                   <  1:258689/139‑1 (MQ=255)

                                                 tAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTa                                                                           <  1:417760/139‑1 (MQ=255)

                                                   agagagCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTaca                                                                         <  2:449804/139‑1 (MQ=255)

                                                         cTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATa                                                                   >  1:323648/1‑139 (MQ=255)

                                                            aTACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGAc                                                                                                            >  1:29371/1‑95 (MQ=255)

                                                            aTACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGAc                                                                                                            <  2:29371/95‑1 (MQ=255)

                                                                      cTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGacaaca                                                      >  1:12463/1‑139 (MQ=255)

                                                                              gTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGaaaaaa                                              >  2:474217/1‑139 (MQ=255)

                                                                                   aaCTTTGATTTACCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGAAAAAAAACCa                                         <  1:316290/139‑1 (MQ=255)

                                                                                         tatttaCCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTAc                                                                                   >  1:601111/1‑91 (MQ=255)

                                                                                         tatttaCCATATTAATGTCAATATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTAc                                                                                   <  2:601111/91‑1 (MQ=255)

                                                                                                            aaTATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAAc                                                                                        >  2:278075/1‑67 (MQ=255)

                                                                                                            aaTATCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAAc                                                                                        <  1:278075/67‑1 (MQ=255)

                                                                                                             atatCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTaca                                                                         <  2:543942/81‑1 (MQ=255)

                                                                                                             atatCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTaca                                                                         >  1:543942/1‑81 (MQ=255)

                                                                                                             atatCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGAAAAAAAACCATACCCAAAAGGTAGTGAATCGTTTGc               >  1:235821/1‑139 (MQ=255)

                                                                                                              tatCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTAc                                                                                   <  2:406716/70‑1 (MQ=255)

                                                                                                              tatCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGacaaca                                                      <  2:309253/99‑1 (MQ=255)

                                                                                                              tatCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGacaaca                                                      >  1:309253/1‑99 (MQ=255)

                                                                                                              tatCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATAAAGACTTGAAAACGCTAc                                                                                   >  1:406716/1‑70 (MQ=255)

                                                                                                               atCGCGTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGAAAAAAAACCATACCCAAAAGGTAGTGAATCGTTTGCtt             <  2:188933/139‑1 (MQ=255)

                                                                                                                   cgTGGATTGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGAAAAAAAACCATACCCAAAAGGTAGTGAATCGTTTGCTTTTaa         >  2:59448/1‑139 (MQ=255)

                                                                                                                          tGAGCGAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGAAAAAAAACCATACCCAAAAGGTAGTGAATCGTTTGCTTTTAACTGGGGa  <  2:323648/139‑1 (MQ=255)

GGAGAAGGTGTTAAGTGATGTCGCCACCAAATCACCCACGCCTATCGCGTAAGAGAGCTGATACGGGGAACTCCAGCTGTTACAACTTTTATTTACCATATTAATGTCAATATCGCGTGGATTGAGCAAAATACGCGATTTGCTCATAGGAAGACGTGTATCAAGACTTGAAAACGCTACCAGTGCTACACAGATACCTAACGACAACAGGAAAAAAAACCATACCCAAAAGGTAGTGAATCGTTTGCTTTTAACTGGGGA  >  NC_000913/4361230‑4361490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A