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 F18 I0 R1	32	69.1	1533550	96.6%	1481409	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,362	G→A	11.1%	H104Y (CAC→TAC)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,362	0	G	A	11.1%	137.6 / 7.5	54	H104Y (CAC→TAC)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base G (23/25); new base A (3/3); total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.87e-01

ATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCG  >  USA300TCH1516_ALE/1744229‑1744502

attATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGtt                                                                                                                                       >  1:446324/1‑141 (MQ=255)

attATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACAAACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGtt                                                                                                                                       <  2:420608/141‑1 (MQ=255)

   ataAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACAGGTTGACCTGGTTTAATTGCATCTTTGTGCTTTGTTaaa                                                                                                                                    >  1:895/1‑141 (MQ=255)

        tGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTATTTTAGAGACAATGATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACAtt                                                                                                                               >  1:557474/1‑141 (MQ=255)

          cactACCGACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTg                                                                                                                             <  1:63236/138‑1 (MQ=255)

          cAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACAttgg                                                                                                                             >  2:687304/1‑139 (MQ=255)

          cAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTg                                                                                                                             <  2:442905/141‑1 (MQ=255)

            aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTGAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGtc                                                                                                                           >  1:526242/1‑140 (MQ=255)

            aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTGATTGCATCTTTGTGCATTCTTAAAACATTTGTa                                                                                                                           >  1:264199/1‑141 (MQ=255)

              aCCTACTACGATACCGCCTAATTTTGCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTAcc                                                                                                                         <  1:636467/141‑1 (MQ=255)

                 tactacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAAGACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCata                                                                                                                      >  2:445282/1‑141 (MQ=255)

                  actacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCGATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACAAACGTTGACCTGGTTTAATTACATCTTTGTGCATTGTTAAAACATTTGTACCatat                                                                                                                     >  2:483468/1‑141 (MQ=255)

                        aTACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTATCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAgg                                                                                                               <  2:14743/141‑1 (MQ=255)

                        aTACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAgg                                                                                                               >  1:185503/1‑141 (MQ=255)

                         tACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGt                                                                                                              >  2:656157/1‑141 (MQ=255)

                                tAATTGTTCAACTAATTTTATTGCTGCTCCAATCGTACCACCAGTAGCTAATAAATTATCTGTAATTAACACACGTTTACCTTGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCGAGGTCATACTc                                                                                                       <  2:253525/141‑1 (MQ=255)

                                 aaTTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCa                                                                                                      >  2:67742/1‑141 (MQ=255)

                                        cAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGaa                                                                                               <  1:484976/141‑1 (MQ=255)

                                        cAACTAATTTTATTGCTGCCTAAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGaa                                                                                               >  1:758861/1‑141 (MQ=255)

                                         aaCTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAAt                                                                                              <  2:297813/141‑1 (MQ=255)

                                          aCTAATTTTATTGCTGCTTCAATCGTACCACCAGGAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATg                                                                                             <  2:89902/141‑1 (MQ=255)

                                              aTTTTAGTGCGGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACtt                                                                                         <  1:68413/141‑1 (MQ=255)

                                                      gctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGt                                                                                 <  1:752722/141‑1 (MQ=255)

                                                            tCAATCGTACCACCAGTAGCGAATAAATCATCCGTCCCTTACACGCGTTGACGTACCTTAATTGCATATTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATCACTTCACGCGGTAATTTc                                                                           >  1:181292/1‑141 (MQ=255)

                                                             cAATCGTACCACCATTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                          <  1:53978/141‑1 (MQ=255)

                                                             cAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTTTCGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                          <  1:369953/141‑1 (MQ=255)

                                                             cAACCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                          <  1:54044/141‑1 (MQ=255)

                                                                tCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAAGTAATTTCCctt                                                                       >  1:660136/1‑141 (MQ=255)

                                                                      caccaGGAGCTAATAAAACATCTGTAATGAACACACGTTTACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTCTTTTc                                                                 <  2:452679/141‑1 (MQ=255)

                                                                       accaGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCAGGCGGTGATTTCCCTTCTTTTCt                                                                >  2:392205/1‑141 (MQ=255)

                                                                          aGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                             <  2:355433/141‑1 (MQ=255)

                                                                           gTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTTATAACGAATGACTTCACGAGGTAATTTTCCTTCTTTTTTAAct                                                            >  1:322574/1‑140 (MQ=255)

                                                                                    aaaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAg                                                   <  2:185503/141‑1 (MQ=255)

                                                                                     aaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTCTTTTCTAACAGGTGCAAAGc                                                  >  2:646447/1‑141 (MQ=255)

                                                                                         atcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAAt                                              >  2:707571/1‑141 (MQ=255)

                                                                                             ttAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcccc                                          <  2:423567/140‑1 (MQ=255)

                                                                                             gTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcccc                                          <  1:209562/141‑1 (MQ=255)

                                                                                              tAATTACCACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                         <  1:343746/141‑1 (MQ=255)

                                                                                              tAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                         <  1:762557/141‑1 (MQ=255)

                                                                                                  tAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGa                                     >  1:628580/1‑141 (MQ=255)

                                                                                                  tAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGa                                     <  1:38570/141‑1 (MQ=255)

                                                                                                    acacacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAAt                                   >  2:209615/1‑141 (MQ=255)

                                                                                                        acGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                               <  1:401790/141‑1 (MQ=255)

                                                                                                        acGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                               <  1:294022/141‑1 (MQ=255)

                                                                                                            tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCACTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACa                           >  1:412464/1‑141 (MQ=255)

                                                                                                            tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAAGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACa                           <  2:660136/141‑1 (MQ=255)

                                                                                                                  ggTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATAACTTCACGAGGTAATTTCCCTTCTTTTCTACCAGGTGCAAAGCCAATCCCCATTGAATCAGCCACAGGACac                     >  2:577620/1‑140 (MQ=255)

                                                                                                                     ttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATACTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCCTTGAATAAGCTACAGGACAGCCa                  >  2:3176/1‑141 (MQ=255)

                                                                                                                         ttGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACGGGACAGCCAATGa              >  1:244787/1‑141 (MQ=255)

                                                                                                                          tGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGAt             <  2:182616/141‑1 (MQ=255)

                                                                                                                            cATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATaa           >  1:645982/1‑141 (MQ=255)

                                                                                                                               cTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGc        <  2:47342/141‑1 (MQ=255)

                                                                                                                               cTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGCCAGCCAATAATAAAGc        >  2:236761/1‑141 (MQ=255)

                                                                                                                                 ttGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCa      <  2:446324/141‑1 (MQ=255)

                                                                                                                                  tgtgCATTGTTAACACATTTGTACCATACTCTAGGTCATACTCATAACGGATGACTTCACGAGTTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGGTAAAGcacc     >  2:529979/1‑138 (MQ=255)

                                                                                                                                     gCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcgcg  <  1:667276/141‑1 (MQ=255)

ATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCG  >  USA300TCH1516_ALE/1744229‑1744502

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