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
A19 F48 I1 R1	83	81.6	2760494	99.1%	2735649	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,457,706	G→T	A444S (GCC→TCC)	gspD →	Type II secretion system protein GspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,457,706	0	G	T	100.0%	192.1 / NA	56	A444S (GCC→TCC)	gspD	Type II secretion system protein GspD
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (29/27); total (29/27)

GGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAACGCAAAACGGTG  >  NC_000913/3457574‑3457837

ggtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCAcccc                                                                                                                              >  1:95291/1‑140 (MQ=255)

         aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGt                                                                                                                     >  1:1292069/1‑140 (MQ=255)

          acAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTa                                                                                                                    <  2:570218/139‑1 (MQ=255)

           cAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTaa                                                                                                                   >  2:977082/1‑140 (MQ=255)

            aGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAAc                                                                                                                  >  1:1344808/1‑140 (MQ=255)

             gcgcGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACg                                                                                                                 <  1:264691/140‑1 (MQ=255)

             gcgcGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACg                                                                                                                 <  1:794932/140‑1 (MQ=255)

             gcgcGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACg                                                                                                                 <  1:34560/140‑1 (MQ=255)

             gcgcGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACg                                                                                                                 <  1:523260/140‑1 (MQ=255)

              cgcgAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGCCCAGTAACAATAAAAATACCATCCCTTCACCCCCAAGCATCTTAACGc                                                                                                                >  2:652938/1‑140 (MQ=255)

               gcgAATCTTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGcg                                                                                                               >  1:1246101/1‑139 (MQ=255)

                cgAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTg                                                                                                              <  2:77988/140‑1 (MQ=255)

                             ggATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTcg                                                                                                 <  2:351069/140‑1 (MQ=255)

                             ggATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTcg                                                                                                 <  1:977082/140‑1 (MQ=255)

                               atatGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTcgcg                                                                                               <  2:598044/140‑1 (MQ=255)

                                   gTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCt                                                                                           >  1:1337079/1‑140 (MQ=255)

                                       aGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCaa                                                                                       >  1:1227055/1‑140 (MQ=255)

                                        gcgcCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAAc                                                                                      >  1:56108/1‑140 (MQ=255)

                                         cgcCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACg                                                                                     <  1:1009740/140‑1 (MQ=255)

                                         cgcCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACg                                                                                     <  1:16056/140‑1 (MQ=255)

                                            cTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTgg                                                                                  >  1:872382/1‑140 (MQ=255)

                                             tACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTtgg                                                                                 >  1:578215/1‑140 (MQ=255)

                                                       tggcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCGCCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGAtgtg                                                                       <  2:578215/140‑1 (MQ=255)

                                                        ggcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGc                                                                      >  2:565380/1‑140 (MQ=255)

                                                         gcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGcc                                                                     >  1:292681/1‑140 (MQ=255)

                                                         gcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGcc                                                                     >  1:1307414/1‑140 (MQ=255)

                                                           agCAGGCTTCTTCAATGGCGACTGGGGACTACTGCTTACCGCGCTAGCCAGTAACAATAAAAATGACATCCACTCCACCCAAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCgg                                                                   <  2:612897/139‑1 (MQ=255)

                                                             cAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGtt                                                                 >  2:212361/1‑139 (MQ=255)

                                                              aGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGc                                                                >  1:1051768/1‑140 (MQ=255)

                                                              aGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGc                                                                >  1:270789/1‑140 (MQ=255)

                                                                 cttcttCAATTGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTAt                                                             <  1:652938/140‑1 (MQ=255)

                                                                         aTGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTca                                                     <  1:565380/140‑1 (MQ=255)

                                                                          tGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTcac                                                    >  2:1195469/1‑140 (MQ=255)

                                                                          tGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTcac                                                    >  2:548419/1‑140 (MQ=255)

                                                                           ggCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTcaca                                                   <  1:846837/140‑1 (MQ=255)

                                                                            gCGACTGGGGAGTACTGCTTACCGCGCAGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAg                                                  >  1:1118715/1‑140 (MQ=255)

                                                                              gACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                <  2:95291/140‑1 (MQ=255)

                                                                              gACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                <  2:1344808/140‑1 (MQ=255)

                                                                              gACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAAAAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                <  2:1264790/140‑1 (MQ=255)

                                                                                cTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCa                                              <  2:991769/140‑1 (MQ=255)

                                                                                     gAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCa                                         <  2:1292069/140‑1 (MQ=255)

                                                                                           tGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGAt                                   >  2:153622/1‑140 (MQ=255)

                                                                                            gCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATa                                  <  2:1307414/140‑1 (MQ=255)

                                                                                             cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAggg                                      >  1:742572/1‑135 (MQ=255)

                                                                                             cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAggg                                      <  2:742572/135‑1 (MQ=255)

                                                                                             cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATaa                                 >  2:414725/1‑140 (MQ=255)

                                                                                             cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATaa                                 >  2:270048/1‑140 (MQ=255)

                                                                                             cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGC‑GGATAATAAACTCGCGTCCTTCAACGTGGGGCAAGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAAc                                <  2:1246101/140‑1 (MQ=255)

                                                                                              ttACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGGCGGTGCTATCCGGGTCACAGACCTCTTCAGGGGATAAc                                <  2:1215056/140‑1 (MQ=255)

                                                                                                aCCGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGt                              >  2:322265/1‑140 (MQ=255)

                                                                                                 ccGCGCTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTc                             <  2:1051768/140‑1 (MQ=255)

                                                                                                      cTGGCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGTTGCTATCCGGGTCACAGACCACTTAAGGGGATAACGTCTTTat                        >  2:76682/1‑139 (MQ=255)

                                                                                                         gCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATAc                     >  2:1342282/1‑140 (MQ=255)

                                                                                                         gCCAGTAACAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATAc                     >  1:773157/1‑140 (MQ=255)

                                                                                                               aaCAATAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGa               <  2:1118715/140‑1 (MQ=255)

                                                                                                                 aaaTAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAAc             <  2:56108/139‑1 (MQ=255)

                                                                                                                   aTAAAAATGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAACGc           >  1:490541/1‑140 (MQ=255)

                                                                                                                      aaaaTGACATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAACGCaaa        <  2:292681/140‑1 (MQ=255)

                                                                                                                            aCATCCTCTCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAACGCAAAACGGTg  >  1:536369/1‑140 (MQ=255)

GGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAACGCAAAACGGTG  >  NC_000913/3457574‑3457837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A