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	757	76.1	3598070	93.4%	3360597	108.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,964,697	G→A	L118L (CTC→CTT)	flhA ←	putative flagellar export pore protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,964,697	0	G	A	100.0%	224.9 / NA	70	L118L (CTC→CTT)	flhA	putative flagellar export pore protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (39/31); total (39/31)

CCCGGCATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAATGGTCGGAAA  >  NC_000913/1964566‑1964831

cccGGCATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGt                                                                                                                                 >  1:866550/1‑139 (MQ=255)

   ggCATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGAc                                                                                                                              >  2:1512809/1‑139 (MQ=255)

      aTACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGa                                                                                                                           >  1:978514/1‑139 (MQ=255)

           aTCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCt                                                                                                                      >  2:846998/1‑139 (MQ=255)

                    aaaGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGaccacc                                                                                                             >  1:765995/1‑139 (MQ=255)

                      aGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCtt                                                                                                           >  2:798140/1‑139 (MQ=255)

                       gcgcgcACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTc                                                                                                          <  2:765995/139‑1 (MQ=255)

                         gcgcACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTccc                                                                                                        >  2:1060760/1‑139 (MQ=255)

                                  cTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTgccgccgc                                                                                               >  2:301976/1‑139 (MQ=255)

                                             cGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTAt                                                                                    >  2:584408/1‑139 (MQ=255)

                                               cccGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAA‑‑‑CACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCt                                                                               <  2:1276075/139‑1 (MQ=255)

                                                ccGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                                                >  1:1791182/1‑108 (MQ=255)

                                                ccGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                                                <  2:1791182/108‑1 (MQ=255)

                                                 cGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                                                <  1:1512809/139‑1 (MQ=255)

                                                 cGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                                                <  2:866550/139‑1 (MQ=255)

                                                 cGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                                                <  1:301976/139‑1 (MQ=255)

                                                                    cATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACgg                                                             >  1:640381/1‑139 (MQ=255)

                                                                     aTAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACggg                                                            <  1:1732238/139‑1 (MQ=255)

                                                                        aaGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTg                                                         <  1:846998/139‑1 (MQ=255)

                                                                           ttGATGATCACGAGAATGACAAACACCACGATACCGTTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCACTTCCATTAAAATGATACGGGTTGAAg                                                      >  2:1797117/1‑139 (MQ=255)

                                                                           ttGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGaa                                                       <  1:676828/138‑1 (MQ=255)

                                                                           ttGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGaa                                                       >  2:676828/1‑138 (MQ=255)

                                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                                                >  2:762945/1‑110 (MQ=255)

                                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                                                <  1:762945/110‑1 (MQ=255)

                                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAtt                                                                         <  1:935826/117‑1 (MQ=255)

                                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAtt                                                                         >  2:935826/1‑117 (MQ=255)

                                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                                          >  2:1022810/1‑116 (MQ=255)

                                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                                          <  1:1022810/116‑1 (MQ=255)

                                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCa                                                   >  1:1658121/1‑139 (MQ=255)

                                                                                  tCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGtt                                               <  1:584408/139‑1 (MQ=255)

                                                                                        gaATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTg                                                         <  2:950325/123‑1 (MQ=255)

                                                                                        gaATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTg                                                         >  1:950325/1‑123 (MQ=255)

                                                                                        gaATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCa                                                   <  1:1336298/129‑1 (MQ=255)

                                                                                        gaATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCa                                                   >  2:1336298/1‑129 (MQ=255)

                                                                                           tGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAg                                      >  1:1294730/1‑139 (MQ=255)

                                                                                              cAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACg                                   >  1:774198/1‑139 (MQ=255)

                                                                                              cAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACg                                   >  1:300372/1‑139 (MQ=255)

                                                                                                   accacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACa                              >  2:758050/1‑139 (MQ=255)

                                                                                                     cacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTc                                                                                                          >  1:681427/1‑61 (MQ=255)

                                                                                                     cacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTc                                                                                                          <  2:681427/61‑1 (MQ=255)

                                                                                                     cacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGc                            >  2:761207/1‑139 (MQ=255)

                                                                                                      acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTaaa                                                                      <  1:639142/96‑1 (MQ=255)

                                                                                                      acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTaaa                                                                      >  2:639142/1‑96 (MQ=255)

                                                                                                      acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCg                           <  1:758050/139‑1 (MQ=255)

                                                                                                       cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcg                                                                                           >  1:774781/1‑74 (MQ=255)

                                                                                                       cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcg                                                                                           <  2:774781/74‑1 (MQ=255)

                                                                                                        gagaCCGATAGCGAAATTGCCACC‑ACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTgccgc                                                                                                  <  2:1737516/62‑1 (MQ=255)

                                                                                                        gATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTg                         <  1:798140/139‑1 (MQ=255)

                                                                                                        gATACCGATAGCGAAATTGCCACC‑ACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTgccgc                                                                                                  >  1:1737516/1‑65 (MQ=255)

                                                                                                         aTACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCt                                                                               <  2:1609858/84‑1 (MQ=255)

                                                                                                         aTACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCt                                                                               >  1:1609858/1‑84 (MQ=255)

                                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGa                                                                                                                  <  1:106492/45‑1 (MQ=255)

                                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGa                                                                                                                  >  2:106492/1‑45 (MQ=255)

                                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTaaa                    >  2:1228103/1‑139 (MQ=255)

                                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCACCGCCGCGCCGGTATGCCCTTCCAt                                                                          >  1:1304907/1‑85 (MQ=255)

                                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCACCGCCGCGCCGGTATGCCCTTCCAt                                                                          <  2:1304907/85‑1 (MQ=255)

                                                                                                               aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGcc                                        <  2:686156/117‑1 (MQ=255)

                                                                                                               aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAaaca                  >  2:1039878/1‑139 (MQ=255)

                                                                                                               aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCATGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGCAGCCACGTTAAGTGcc                                        >  1:686156/1‑117 (MQ=255)

                                                                                                                  gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACggg                                                            <  2:1132315/94‑1 (MQ=255)

                                                                                                                  gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACggg                                                            >  1:1132315/1‑94 (MQ=255)

                                                                                                                  gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAacaaca               >  2:1031840/1‑139 (MQ=255)

                                                                                                                    gAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTaaa                                                                      <  1:435618/82‑1 (MQ=255)

                                                                                                                    gAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTaaa                                                                      >  2:435618/1‑82 (MQ=255)

                                                                                                                    gAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGa             <  2:259391/139‑1 (MQ=255)

                                                                                                                       aTTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTaa                                             >  2:1691718/1‑104 (MQ=255)

                                                                                                                       aTTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTaa                                             <  1:1691718/104‑1 (MQ=255)

                                                                                                                           ccaccaACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                                            >  2:1704035/1‑53 (MQ=255)

                                                                                                                           ccaccaACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                                            <  1:1704035/53‑1 (MQ=255)

                                                                                                                            caccaACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAATGGTCgg     <  2:640381/139‑1 (MQ=255)

                                                                                                                               caacaaGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAATGGTCGGaaa  >  2:1765122/1‑139 (MQ=255)

CCCGGCATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAATGGTCGGAAA  >  NC_000913/1964566‑1964831

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A