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
A5 F58 I0 R1	46	56.2	1222162	96.0%	1173275	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	382,916	C→A	23.0%	G331C (GGT→TGT)	ulaA ←	Ascorbate‑specific PTS system EIIC component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	382,916	0	C	A	23.0%	124.2 / 24.6	59	G331C (GGT→TGT)	ulaA	Ascorbate‑specific PTS system EIIC component
Reads supporting (aligned to +/- strand): ref base C (19/26); new base A (9/5); total (28/31)
Fisher's exact test for biased strand distribution p-value = 2.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTTAGAGCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGACG  >  USA300TCH1516_ALE/382776‑383052

aTTTAGAGCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATAcc                                                                                                                                          >  2:511332/1‑141 (MQ=255)

   tAGAGCGGCGACAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGAt                                                                                                                                       >  1:442314/1‑141 (MQ=255)

    agagCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATg                                                                                                                                      >  1:327925/1‑141 (MQ=255)

     gagCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGa                                                                                                                                     >  2:529949/1‑141 (MQ=255)

          gcgcCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCt                                                                                                                                <  2:64162/141‑1 (MQ=255)

           cgcCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATACGATAAACATACCGATGACACCTg                                                                                                                               <  2:283133/141‑1 (MQ=255)

            gcCAGCAATAGCACCTTTAATACCGCCTCTTTCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGt                                                                                                                              <  2:248366/141‑1 (MQ=255)

                gCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGtaata                                                                                                                          >  1:134106/1‑141 (MQ=255)

                 cAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAACCATACCGATGACACCAGtaataa                                                                                                                         >  1:487806/1‑141 (MQ=255)

                        aCCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGAc                                                                                                                  <  1:381002/141‑1 (MQ=255)

                           tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa                                                                                                               <  2:130340/141‑1 (MQ=255)

                           tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa                                                                                                               >  2:553582/1‑141 (MQ=255)

                           tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa                                                                                                               >  1:407147/1‑141 (MQ=255)

                           tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa                                                                                                               >  1:402019/1‑141 (MQ=255)

                           tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCAACAAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa                                                                                                               >  2:553532/1‑141 (MQ=255)

                            ttAATACCGCCTCTGGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAg                                                                                                              >  1:424178/1‑141 (MQ=255)

                                 aCCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATcc                                                                                                         >  2:104522/1‑141 (MQ=255)

                                   cGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACGAAGAATCCaa                                                                                                       <  1:442326/141‑1 (MQ=255)

                                        ctTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTCCGCCCGGTAAAATGACGACGCCACCAAATAAGAATACCAAAAACATACAGATGCCACCTGTAATAAAGCAGAAAAAGAACCCAATTAAt                                                                                                  >  1:275191/1‑141 (MQ=255)

                                         ttGCATTACCTAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATa                                                                                                 <  2:241904/141‑1 (MQ=255)

                                           gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACt                                                                                               <  2:329746/141‑1 (MQ=255)

                                           gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGGAATAAAGCTGACAAAGAATCCAATTAATACt                                                                                               >  1:274444/1‑141 (MQ=255)

                                           gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACt                                                                                               <  1:22640/141‑1 (MQ=255)

                                           gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAACAAGAATAAGATAAACATACAGAAGACACCGGTAAAAAAACTCACAAAGAATCCAATTAATAca                                                                                               >  2:446569/1‑140 (MQ=255)

                                            cATGACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACCACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTg                                                                                              <  1:189922/141‑1 (MQ=255)

                                               tACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCAt                                                                                           <  2:53621/141‑1 (MQ=255)

                                                    aaTACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTtgt                                                                                      >  1:252604/1‑141 (MQ=255)

                                                       aCAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGAAAAATGACGCCGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCCATTAATACTGCATTTTGTGCa                                                                                   >  2:100037/1‑141 (MQ=255)

                                                           caggCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACGCCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCCTatg                                                                               >  1:439072/1‑139 (MQ=255)

                                                           cagcCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAg                                                                               <  1:537377/141‑1 (MQ=255)

                                                           cagcCGCTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAg                                                                               <  1:537473/141‑1 (MQ=255)

                                                             actggtccACCTAAGAAGAAGCGTGCAACTACGCCAGGTAAAATGCCGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATCCTGCATTTTGTGCATAAggg                                                                             >  2:462449/8‑141 (MQ=255)

                                                                  tGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAacac                                                                        >  2:605194/1‑141 (MQ=255)

                                                                   gCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATCAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAGcaca                                                                       >  2:355222/1‑141 (MQ=255)

                                                                      ccTAAGAAGAAGGGTGCAACTACGGCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAGTAAAGCTGACAAAGAATCCCATTAATACTGCATTTTGTGCATAAGGGAACACAATa                                                                    <  1:115110/141‑1 (MQ=255)

                                                                         aagaagaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAggg                                                                 <  2:14818/141‑1 (MQ=255)

                                                                         aagaagaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAggg                                                                 <  1:488121/141‑1 (MQ=255)

                                                                             agaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCACTTAATACTGCATTTTGTGCATAAGGGAACACAATAGAGCAGt                                                             >  2:390640/1‑141 (MQ=255)

                                                                             aaaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGt                                                             <  1:574685/139‑1 (MQ=255)

                                                                                agTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTa                                                          <  2:110512/141‑1 (MQ=255)

                                                                                agTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTa                                                          >  1:517478/1‑141 (MQ=255)

                                                                                 gtgtGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTaa                                                         <  2:63438/141‑1 (MQ=255)

                                                                                   gtgCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATg                                                       <  2:442851/141‑1 (MQ=255)

                                                                                     gCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCa                                                     <  1:97398/141‑1 (MQ=255)

                                                                                         cTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAAAAGGGCAGTCTAATGCAGGtt                                                 <  1:370274/141‑1 (MQ=255)

                                                                                                   tAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTgg                                       >  1:486580/1‑141 (MQ=255)

                                                                                                              ctccaccaACTAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCtttt                            <  1:195763/139‑1 (MQ=255)

                                                                                                              cgCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCtttt                            <  1:22403/141‑1 (MQ=255)

                                                                                                              cgCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCtttt                            >  1:161338/1‑141 (MQ=255)

                                                                                                                 caccaAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAg                         <  1:355222/141‑1 (MQ=255)

                                                                                                                     aaaTAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAAt                     <  1:529949/141‑1 (MQ=255)

                                                                                                                        taagaataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGGACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTct                  >  1:43583/1‑140 (MQ=255)

                                                                                                                          agaataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCtt                >  2:455311/1‑141 (MQ=255)

                                                                                                                           gaataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCttt               <  1:244702/141‑1 (MQ=255)

                                                                                                                           gaataagaTAAACATACAGATGACACGAGTAATAAAGCTGACAAAGAATACAATTAATACTGCATTTTGTACATAAGAGAACACGATAGGGCCGACTAATACAGGATCAGAATTTGGTACAAGCTTTTCAGGAATTGCttt               >  2:16168/1‑141 (MQ=255)

                                                                                                                            aataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTa              <  1:241939/141‑1 (MQ=255)

                                                                                                                            aataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTa              <  1:605194/141‑1 (MQ=255)

                                                                                                                                  aTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCt        <  1:583916/141‑1 (MQ=255)

                                                                                                                                      aCATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGa    >  2:494052/1‑141 (MQ=255)

                                                                                                                                        aTACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGACg  <  2:517478/141‑1 (MQ=255)

ATTTAGAGCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGACG  >  USA300TCH1516_ALE/382776‑383052

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A