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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,319,473	G→A	P45L (CCG→CTG)	phnJ ←	carbon‑phosphorus lyase, SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,319,473	0	G	A	100.0%	119.0 / NA	38	P45L (CCG→CTG)	phnJ	carbon‑phosphorus lyase, SAM‑dependent
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (16/22); total (16/22)

CGCTTGAAGAAGTTGCGAATCGACACGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACGGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCTCAGA  >  NC_000913/4319344‑4319598

cgcTTGAAGAAGTTGCGAATCGACACGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTAcagcatcggca                                                                                                                      >  1:261006/1‑139 (MQ=255)

     gaagaaGTTGCGAATCGACACGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTcg                                                                                                                 <  2:261006/139‑1 (MQ=255)

              gCGAATCGACACGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTT‑‑CCAGCCGTACAGCATCGGCATCTCGCGCCCGCCaaa                                                                                                      <  2:248337/139‑1 (MQ=255)

                   tCGACACGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACgg                                                                                                   <  2:774650/139‑1 (MQ=255)

                    cGACACGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGc                                                                                                  <  1:787110/139‑1 (MQ=255)

                       cacGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATGACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCAcc                                                                                               <  1:699293/139‑1 (MQ=255)

                                      gtCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATc                                                                                >  1:38667/1‑139 (MQ=255)

                                          tCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCa                                                                            <  1:860696/139‑1 (MQ=255)

                                          tCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCa                                                                            <  1:204268/139‑1 (MQ=255)

                                              cgcCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACgg                                                                                                   <  1:1044337/112‑1 (MQ=255)

                                              cgcCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTACCCAGCCGTACAGCCTCGGCATCTCGCGCCCGCCAAACgg                                                                                                   >  2:1044337/1‑112 (MQ=255)

                                                   tGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTa                                                                   <  2:38667/139‑1 (MQ=255)

                                                    ggTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTaa                                                                  >  2:166958/1‑139 (MQ=255)

                                                     gTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAg                                                                 >  2:354685/1‑139 (MQ=255)

                                                        aaTCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATg                                                              >  1:226386/1‑139 (MQ=255)

                                                         aTCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATgg                                                             >  2:635479/1‑139 (MQ=255)

                                                          tCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGgc                                                            >  1:190346/1‑139 (MQ=255)

                                                           cACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGgcg                                                           <  2:226386/139‑1 (MQ=255)

                                                                    cACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATc                                                  >  1:689824/1‑139 (MQ=255)

                                                                        tCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGa                                                                                            <  1:1070213/93‑1 (MQ=255)

                                                                        tCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGa                                                                                            >  2:1070213/1‑93 (MQ=255)

                                                                         cGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCg                                             >  1:81324/1‑139 (MQ=255)

                                                                            tttCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGttt                                          >  1:951942/1‑139 (MQ=255)

                                                                                          cTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGa                            >  2:895752/1‑139 (MQ=255)

                                                                                              cGGTAAGCTGAATGCTGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCa                                                                            >  2:744348/1‑87 (MQ=255)

                                                                                              cGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCa                                                                            <  1:744348/87‑1 (MQ=255)

                                                                                                gTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAgg                      <  2:362428/139‑1 (MQ=255)

                                                                                                       gAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCAc                                                                           >  2:184553/1‑79 (MQ=255)

                                                                                                       gAATGCCGCCGGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCAc                                                                           <  1:184553/79‑1 (MQ=255)

                                                                                                             cgccgGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACgg                                                                                                   >  2:1035685/1‑49 (MQ=255)

                                                                                                             cgccgGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACgg                                                                                                   <  1:1035685/49‑1 (MQ=255)

                                                                                                             cgccgGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCC‑AACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCg        <  1:167456/139‑1 (MQ=255)

                                                                                                              gccgGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCg        <  2:951942/139‑1 (MQ=255)

                                                                                                                cgGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCt      <  2:190346/139‑1 (MQ=255)

                                                                                                                cgGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCt      <  1:354685/139‑1 (MQ=255)

                                                                                                                cgGTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCt      <  2:689824/139‑1 (MQ=255)

                                                                                                                  gTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCTCa    <  1:648790/139‑1 (MQ=255)

                                                                                                                  gTTCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCTCa    >  1:340811/1‑139 (MQ=255)

                                                                                                                    tCCCCAGCCGTACAGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCTCAGa  <  2:81324/139‑1 (MQ=255)

CGCTTGAAGAAGTTGCGAATCGACACGGCGTTGGTGGTGTCATCCGCGCCCTGGTCAATCACCTTCAGCACGTCGCTTTCGCCAATCACGCTGGCGGTAAGCTGAATGCCGCCGGTTCCCCAGCCGTACGGCATCGGCATCTCGCGCCCGCCAAACGGCACCTGATAACCGGGGATCGCCACCGCTTTTAAGATGGCGCGGCGGATCATGCGTTTGGTCTGCTCGTCGAGGTAGGCAAAGTTGTAGCCGCTCAGA  >  NC_000913/4319344‑4319598

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