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	92	50.6	2362856	94.3%	2228173	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,657,767	G→A	C68Y (TGC→TAC)	ynfD →	DUF1161 family periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,657,767	0	G	A	100.0%	170.8 / NA	48	C68Y (TGC→TAC)	ynfD	DUF1161 family periplasmic protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (30/18); total (30/18)

GTGAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTGCGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGATAT  >  NC_000913/1657641‑1657896

gtgAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       <  2:321790/139‑1 (MQ=255)

gtgAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       <  1:326977/139‑1 (MQ=255)

            agagCGATATATCAAAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAAGtct                                                                                                           <  1:18285/139‑1 (MQ=255)

              agCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTctct                                                                                                         >  1:1061065/1‑139 (MQ=255)

                             cgcATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          >  2:274384/1‑139 (MQ=255)

                             cgcATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          >  1:691850/1‑139 (MQ=255)

                               cATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGc                                                                                        >  1:384627/1‑139 (MQ=255)

                                            ggCGTACCCGAAAGCAGCTTCACGTTAAGAATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTAGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTg                                                                           >  2:788124/1‑139 (MQ=255)

                                              cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGc                                                                                                 <  2:1067321/115‑1 (MQ=255)

                                              cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGc                                                                                                 >  1:1067321/1‑115 (MQ=255)

                                              cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCgg                                                                                      >  2:449072/1‑126 (MQ=255)

                                              cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCgg                                                                                      <  1:449072/126‑1 (MQ=255)

                                              cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCt                                                                         <  1:788124/139‑1 (MQ=255)

                                              cGTACCCGAAAGCAGATTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCt                                                                         >  1:786707/1‑139 (MQ=255)

                                                tACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCGGCACCACCAGCGGTAACGTCTCTGCTcc                                                                       >  2:706697/1‑139 (MQ=255)

                                                        agcagcTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               <  1:1032753/139‑1 (MQ=255)

                                                        agcagcTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               <  1:869109/139‑1 (MQ=255)

                                                             cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTa                                                                                                                              >  2:144379/1‑71 (MQ=255)

                                                             cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTa                                                                                                                              <  1:144379/71‑1 (MQ=255)

                                                             cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGc                                                          >  1:970637/1‑139 (MQ=255)

                                                             cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGc                                                          >  2:908365/1‑139 (MQ=255)

                                                                            tGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               <  1:847642/119‑1 (MQ=255)

                                                                            tGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               >  2:847642/1‑119 (MQ=255)

                                                                             gTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGAt                                                                                                                         <  1:884646/60‑1 (MQ=255)

                                                                             gTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGAt                                                                                                                         >  2:884646/1‑60 (MQ=255)

                                                                              tACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGc                                         >  1:878240/1‑139 (MQ=255)

                                                                                cccAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCg                                       >  2:350926/1‑139 (MQ=255)

                                                                                 ccAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          >  2:140792/1‑87 (MQ=255)

                                                                                 ccAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          <  1:140792/87‑1 (MQ=255)

                                                                                   aaTGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCCGTCTAGCCAGGATGGCGCGCCTGCCGAAc                                    <  2:786707/139‑1 (MQ=255)

                                                                                     tGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCg                                  >  2:1151814/1‑139 (MQ=255)

                                                                                     tGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCg                                  <  2:878240/139‑1 (MQ=255)

                                                                                            gTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAac                           >  1:1098214/1‑139 (MQ=255)

                                                                                                aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       <  2:982928/43‑1 (MQ=255)

                                                                                                aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       >  1:982928/1‑43 (MQ=255)

                                                                                                aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCcgcg                                                                   <  2:1082061/95‑1 (MQ=255)

                                                                                                aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCcgcg                                                                   >  1:1082061/1‑95 (MQ=255)

                                                                                                 tCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACAtt                      >  2:272077/1‑139 (MQ=255)

                                                                                                 tCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACAtt                      >  1:557563/1‑139 (MQ=255)

                                                                                                     ccTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCg                  >  1:243269/1‑139 (MQ=255)

                                                                                                          ttCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGa             >  2:70200/1‑139 (MQ=255)

                                                                                                                    gtcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCg                                       <  2:431327/103‑1 (MQ=255)

                                                                                                                    gtcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCg                                       >  1:431327/1‑103 (MQ=255)

                                                                                                                     tcgGCCATTACGCTAATGGTACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGatat  >  2:1135787/1‑139 (MQ=255)

                                                                                                                     tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGt                                                                                <  1:944156/61‑1 (MQ=255)

                                                                                                                     tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGt                                                                                >  2:944156/1‑61 (MQ=255)

                                                                                                                     tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGatat  >  2:230407/1‑139 (MQ=255)

                                                                                                                     tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGatat  >  2:190184/1‑139 (MQ=255)

GTGAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTGCGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGATAT  >  NC_000913/1657641‑1657896

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A