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
A11 F1 I1 R1	63	64.8	2934156	93.7%	2749304	111.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,534,920	G→A	R317W (CGG→TGG)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,534,920	0	G	A	100.0%	158.0 / NA	47	R317W (CGG→TGG)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (24/23); total (24/23)

TTCCGCTGCTGACTTTGATCCAGCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCACTCTTCGATAT  >  NC_000913/3534785‑3535051

ttCCGCTGCTGACTTTGATCCAGCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTc                                                                                                                                  >  1:1425043/1‑139 (MQ=255)

              ttGATCCAGCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCgg                                                                                                                    <  2:1260229/139‑1 (MQ=255)

                     aGCCCTTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAAt                                                                                                             >  1:1337229/1‑139 (MQ=255)

                      gCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAAtc                                                                                                            >  1:1061894/1‑139 (MQ=255)

                         aTTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAAtcacc                                                                                                         <  1:160953/139‑1 (MQ=255)

                         aTTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAAtcacc                                                                                                         <  1:276684/139‑1 (MQ=255)

                           tGCCATAACGGGCGGGGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTGAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAAtcacctc                                                                                                       >  2:979568/1‑139 (MQ=255)

                                tAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGa                                                                                                  >  1:122898/1‑139 (MQ=255)

                                  aCGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGt                                                                                                >  1:851139/1‑139 (MQ=255)

                                   cGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTa                                                                                               <  2:122898/139‑1 (MQ=255)

                                     ggcggcGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACt                                                                                             >  1:1318455/1‑139 (MQ=255)

                                                         tCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAAtcacc                                                                                                         <  2:1225798/107‑1 (MQ=255)

                                                         tCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAAtcacc                                                                                                         >  1:1225798/1‑107 (MQ=255)

                                                           gCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCa                                                                       <  2:851139/139‑1 (MQ=255)

                                                             cACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATc                                                                     >  1:465297/1‑139 (MQ=255)

                                                                  cgcgTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCAt                                                                >  2:238554/1‑139 (MQ=255)

                                                                  cgcgTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCAt                                                                >  2:382724/1‑139 (MQ=255)

                                                                  cgcgTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCAt                                                                >  2:1034894/1‑139 (MQ=255)

                                                                          aTCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGcc                                                        <  2:1318455/139‑1 (MQ=255)

                                                                                 gCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTgcg                                                 >  2:341416/1‑139 (MQ=255)

                                                                                    ggTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTa                                                                                               >  1:806713/1‑90 (MQ=255)

                                                                                    ggTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTa                                                                                               <  2:806713/90‑1 (MQ=255)

                                                                                     gTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTCAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAgg                                             >  1:375757/1‑139 (MQ=255)

                                                                                      tGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGt                                            <  2:607340/139‑1 (MQ=255)

                                                                                      tGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGt                                            <  1:238554/139‑1 (MQ=255)

                                                                                            ttCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTa                                                                                               <  1:566157/82‑1 (MQ=255)

                                                                                            ttCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGa                                      >  1:1330552/1‑139 (MQ=255)

                                                                                            ttCACCTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCATTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTa                                                                                               >  2:566157/1‑82 (MQ=255)

                                                                                                cTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATaaa                                  <  1:1343770/139‑1 (MQ=255)

                                                                                                  tCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACttt                                                                                                                       >  1:1128805/1‑52 (MQ=255)

                                                                                                  tCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACttt                                                                                                                       <  2:1128805/52‑1 (MQ=255)

                                                                                                   cAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTg                               <  2:1337229/139‑1 (MQ=255)

                                                                                                           ccGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGt                                                                                                <  2:185862/66‑1 (MQ=255)

                                                                                                           ccGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGt                                                                                                >  1:185862/1‑66 (MQ=255)

                                                                                                           ccGGGGTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAatga                       <  2:987498/139‑1 (MQ=255)

                                                                                                                gTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGgcagc                                                                                                                <  2:901720/45‑1 (MQ=255)

                                                                                                                gTAAAGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGgaagc                                                                                                                >  1:901720/1‑45 (MQ=255)

                                                                                                                   aaGCGCGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTg               <  2:1330552/139‑1 (MQ=255)

                                                                                                                     gcgcGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCa             <  2:375757/139‑1 (MQ=255)

                                                                                                                     gcgcGGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGAT‑AACTGCTCAATGATGGCGTTGCAc            >  1:281164/1‑139 (MQ=255)

                                                                                                                      cgcgTTTTCAATTTCCCACTCAGAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCAc            <  2:951648/139‑1 (MQ=255)

                                                                                                                        cgGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAg                                                                                                 <  2:454683/52‑1 (MQ=255)

                                                                                                                        cgGTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAg                                                                                                 >  1:454683/1‑52 (MQ=255)

                                                                                                                         ggTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTg                                                   <  1:826772/97‑1 (MQ=255)

                                                                                                                         ggTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTg                                                   >  2:826772/1‑97 (MQ=255)

                                                                                                                          gTTTCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCACTCtt        >  2:614476/1‑139 (MQ=255)

                                                                                                                             tCAATTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCACTCTTCGa     <  2:817915/139‑1 (MQ=255)

                                                                                                                                aTTTCCCACTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCACTCTTCGatat  <  2:1061894/139‑1 (MQ=255)

TTCCGCTGCTGACTTTGATCCAGCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCACTCTTCGATAT  >  NC_000913/3534785‑3535051

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