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 I2 R1	777	59.2	2955938	92.5%	2734242	106.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,082,038	T→C	D42D (GAT→GAC)	loiP →	Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,082,038	0	T	C	100.0%	221.0 / NA	61	D42D (GAT→GAC)	loiP	Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (32/29); total (32/29)

AAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAGGCAACAATATC  >  NC_000913/3081908‑3082164

aaaaCATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCa                                                                                                                           >  1:102690/1‑136 (MQ=255)

aaaaCATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCa                                                                                                                           <  2:102690/136‑1 (MQ=255)

     aTGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGaaaa                                                                                                                   >  1:618213/1‑139 (MQ=255)

        aaaaTTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAAccc                                                                                                                >  1:505858/1‑139 (MQ=255)

              cgcgCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCg                                                                                                          >  2:543474/1‑139 (MQ=255)

                   cTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAg                                                                                                     <  2:855905/139‑1 (MQ=255)

                    ttATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                                    <  2:1456747/139‑1 (MQ=255)

                       ttGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCAACAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCAt                                                                                                 <  1:1194937/139‑1 (MQ=255)

                          gTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTc                                                                                              <  2:242081/139‑1 (MQ=255)

                            aGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAg                                                                                            <  2:505858/139‑1 (MQ=255)

                               aaTGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGgag                                                                                         >  1:118281/1‑139 (MQ=255)

                               aaTGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGgag                                                                                         >  1:632111/1‑139 (MQ=255)

                                 tGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGAt                                                                                       >  1:705239/1‑139 (MQ=255)

                                 tGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGAt                                                                                       >  1:971109/1‑139 (MQ=255)

                                   aGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATgg                                                                                     >  2:793560/1‑139 (MQ=255)

                                    gCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTc                                                                                              <  2:1421785/129‑1 (MQ=255)

                                    gCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTc                                                                                              >  1:1421785/1‑129 (MQ=255)

                                    gCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGa                                                                                    <  1:543474/139‑1 (MQ=255)

                                        ggCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGc                                                                                <  1:793560/139‑1 (MQ=255)

                                                          ttGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcca                                                              >  2:425590/1‑139 (MQ=255)

                                                          ttGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcca                                                              >  1:491912/1‑139 (MQ=255)

                                                          ttGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcca                                                              >  2:469868/1‑139 (MQ=255)

                                                            gCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagc                                                            >  2:891028/1‑139 (MQ=255)

                                                              cAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgccagcca                                                          <  2:1169602/139‑1 (MQ=255)

                                                                   tatGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                                    <  2:759128/92‑1 (MQ=255)

                                                                   tatGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAgg                                                                                                    >  1:759128/1‑92 (MQ=255)

                                                                   tatGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGc                                                     >  2:425710/1‑139 (MQ=255)

                                                                          tCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAACGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACg                                              >  1:1051349/1‑139 (MQ=255)

                                                                            cAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCt                                            >  2:1397569/1‑139 (MQ=255)

                                                                                  aCTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGATAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGt                                      <  1:891028/139‑1 (MQ=255)

                                                                                      ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGaa                                                                                                                     >  2:1173260/1‑56 (MQ=255)

                                                                                      ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGaa                                                                                                                     <  1:1173260/56‑1 (MQ=255)

                                                                                      ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGa                                                                                                         >  2:1455022/1‑68 (MQ=255)

                                                                                      ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGa                                                                                                         <  1:1455022/68‑1 (MQ=255)

                                                                                      ctctCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGa                                  >  1:834343/1‑139 (MQ=255)

                                                                                       tctcATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGAc                                 <  2:834343/139‑1 (MQ=255)

                                                                                       tctcATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGAc                                 <  2:911643/139‑1 (MQ=255)

                                                                                        ctcATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcca                                                              <  1:791452/109‑1 (MQ=255)

                                                                                        ctcATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcca                                                              >  2:791452/1‑109 (MQ=255)

                                                                                                gAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACg                                       >  2:425290/1‑124 (MQ=255)

                                                                                                gAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACg                                       <  1:425290/124‑1 (MQ=255)

                                                                                                gAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGc                        >  1:1223342/1‑139 (MQ=255)

                                                                                                gAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGc                        >  1:189135/1‑139 (MQ=255)

                                                                                                     gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTg                                                                                                              >  2:1257107/1‑48 (MQ=255)

                                                                                                     gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTg                                                                                                              <  1:1257107/48‑1 (MQ=255)

                                                                                                     gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTc                                                                                              <  1:76398/64‑1 (MQ=255)

                                                                                                     gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTc                                                                                              >  2:76398/1‑64 (MQ=255)

                                                                                                     gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATg                   >  1:85459/1‑139 (MQ=255)

                                                                                                     gAAGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATg                   <  1:561163/139‑1 (MQ=255)

                                                                                                       aGCTTTTCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgcg                 <  1:586467/139‑1 (MQ=255)

                                                                                                           tttCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcc                                                               >  1:1015698/1‑89 (MQ=255)

                                                                                                           tttCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCgcc                                                               <  2:1015698/89‑1 (MQ=255)

                                                                                                             tCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAGGc           <  2:618213/139‑1 (MQ=255)

                                                                                                             tCAGGCTTACAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAGGc           <  1:322643/139‑1 (MQ=255)

                                                                                                                      cAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATa                                                <  2:55653/93‑1 (MQ=255)

                                                                                                                      cAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATa                                                >  1:55653/1‑93 (MQ=255)

                                                                                                                      cAGTTTGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAGGCAACAATATc  <  1:425710/139‑1 (MQ=255)

                                                                                                                           tGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgcg                 >  1:1327555/1‑119 (MQ=255)

                                                                                                                           tGAGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATgcg                 <  2:1327555/119‑1 (MQ=255)

                                                                                                                             aGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGc                                                                                >  1:1466044/1‑54 (MQ=255)

                                                                                                                             aGTGACGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGc                                                                                <  2:1466044/54‑1 (MQ=255)

AAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGCGGAAGCTTTTCAGGCTTACAGTTTGAGTGATGCGCAGGTGAAAACCCTGAGCGATCAGGCATGTCAGGAGATGGACAGCAAGGCGACGATTGCGCCAGCCAATAGCGAATACGCTAAACGTCTGACAACTATTGCCAATGCGCTAGGCAACAATATC  >  NC_000913/3081908‑3082164

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `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