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	1,744,362	G→A	19.0%	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	19.0%	100.8 / 22.5	54	H104Y (CAC→TAC)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base G (17/26); new base A (5/5); total (22/32)
Fisher's exact test for biased strand distribution p-value = 7.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.27e-01

TATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACG  >  USA300TCH1516_ALE/1744231‑1744500

tataAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTaa                                                                                                                                   >  2:542485/1‑141 (MQ=255)

  taAATGCAATACCTACTACCATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTaaaa                                                                                                                                 <  1:485213/141‑1 (MQ=255)

   aaaTGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAAc                                                                                                                                >  2:103427/1‑141 (MQ=255)

          aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTa                                                                                                                         >  2:226772/1‑141 (MQ=255)

          aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTa                                                                                                                         <  1:547114/141‑1 (MQ=255)

              ctactaCGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCat                                                                                                                     <  1:155019/141‑1 (MQ=255)

                 ctacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCTTAtt                                                                                                                  <  2:422881/141‑1 (MQ=255)

                   acaaaaCCGCCTAATCTTTCAACTAAACATATTGCCGCTCCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCt                                                                                                                <  1:182607/136‑1 (MQ=255)

                     gATACCGCCTAATTTTTCAACTAATTCTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAATACATTTGTACCATATTCTAg                                                                                                              <  1:371331/141‑1 (MQ=255)

                       tACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTTAAACATTTGTACCATATTCTAGGt                                                                                                            <  1:446365/141‑1 (MQ=255)

                       tACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACCTTTATTTTTTTTAATTGCATCTTTGTGCATTGTTTAAACATTTGTACCATATTCTAGGt                                                                                                            <  1:446465/141‑1 (MQ=255)

                        aCCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTc                                                                                                           <  1:88511/141‑1 (MQ=255)

                         cccccTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                          <  2:59362/138‑1 (MQ=255)

                         ccGCCTAATTTTTCAACTAATTTTATTGATGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                          >  1:448992/1‑141 (MQ=255)

                          cGCCGAATTTTTCAACTACTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTTACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCAt                                                                                                         <  1:510520/141‑1 (MQ=255)

                                 tttttCAATTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGCTTAATTGCATCTTTGTGCATTGCTAAAACATTTGTACCATATTCTAGGTCATACTCAtt                                                                                                  <  2:145446/141‑2 (MQ=255)

                                     tCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATGCTCATAACGa                                                                                              >  2:89948/1‑141 (MQ=255)

                                      cAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTTCATCTTTGTGCATTGTTAAAACATTTGTCCCATATTCTAGGTCATCATCATAACGaa                                                                                             >  1:45766/1‑141 (MQ=255)

                                        aCTAATTTTATTGCTGTTTCAATCGTACCATTATTATCTAATAATTCATCTGTAATTAACATACGTTGACCTGTTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGTTCATACTCATAACGAATg                                                                                           <  2:60310/141‑1 (MQ=255)

                                          tAATTTTATTCCTCCTTCAATCGTACCACCAGTAGCTAATAAATCATCAGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGAc                                                                                         <  2:147501/141‑1 (MQ=255)

                                           aactttATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACt                                                                                        <  2:441928/138‑1 (MQ=255)

                                           aaTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTTTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACt                                                                                        >  1:501079/1‑141 (MQ=255)

                                                 aTTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGa                                                                                  <  1:103427/141‑1 (MQ=255)

                                                 aTTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGa                                                                                  >  2:57618/1‑141 (MQ=255)

                                                      tgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTaa                                                                             >  2:187224/1‑141 (MQ=255)

                                                          tCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTc                                                                         <  1:355631/141‑1 (MQ=255)

                                                           cactCGTACCACCTGTAGCTTATAATTCATCTGTTATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                        <  1:5596/138‑1 (MQ=255)

                                                           cAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                        <  2:508378/141‑1 (MQ=255)

                                                           cAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                        <  1:511883/141‑1 (MQ=255)

                                                            aaTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTccc                                                                       <  2:104784/141‑1 (MQ=255)

                                                              tCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCctt                                                                     >  2:297288/1‑141 (MQ=255)

                                                                  accaccAGTAGCTAATAAATCATCTGTAAGTAACACACGTTGACCTGGTTTAATTGAATCTTTGTACATTGTTAAAACATTTGTACAATAATCTAGTTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCttt                                                                 >  2:398746/1‑141 (MQ=255)

                                                                    caccaGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATACCGCAAGACTTCACGAGGGACCTTACCTTCTTTTc                                                               >  2:263577/1‑141 (MQ=255)

                                                                       caGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTaa                                                            >  2:285697/1‑141 (MQ=255)

                                                                        attAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                           <  2:263082/139‑1 (MQ=255)

                                                                        aGTAGCTAATAAATCATCTGTTATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                           <  2:596050/141‑1 (MQ=255)

                                                                        aGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                           <  1:179976/141‑1 (MQ=255)

                                                                               aataaATCATCTGTAAATAAGACATGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGGAATTTCCCTTCTTTTCTAACAGTTGCa                                                    >  2:282233/1‑141 (MQ=255)

                                                                                ataaATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGATGCaa                                                   >  1:131065/1‑141 (MQ=255)

                                                                                  aaaTCATCTTTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTCCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACGTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAg                                                 <  2:99367/141‑1 (MQ=255)

                                                                                      cagcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCaa                                             <  1:259000/138‑1 (MQ=255)

                                                                                          tGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATccc                                         >  1:557830/1‑141 (MQ=255)

                                                                                            tAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                       <  2:607926/141‑1 (MQ=255)

                                                                                                 aaCACACGTTTACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGaa                                  <  2:592928/141‑1 (MQ=255)

                                                                                                  acacacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTCCCCTATTCTCGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGTCAATCCAATCCCCATTGAAt                                 >  1:210924/1‑141 (MQ=255)

                                                                                                      acGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTACAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                             <  1:397982/141‑1 (MQ=255)

                                                                                                      acGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                             <  2:195125/141‑1 (MQ=255)

                                                                                                          tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATTACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACa                         >  1:189792/1‑141 (MQ=255)

                                                                                                             ccTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACTATATTCTAGGTCATCCTCATAGCGAATGACTTAACGAGGTTATTTTCCTTCTTTTCTAACAGGTGGAAAGGCATTATCCATAGAATTAGTTACAGGa                      >  2:846/1‑141 (MQ=255)

                                                                                                               tGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACa                    >  1:522033/1‑141 (MQ=255)

                                                                                                                  tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGcc                 >  2:85268/1‑141 (MQ=255)

                                                                                                                  tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGcc                 >  2:103678/1‑141 (MQ=255)

                                                                                                                     aatgtcATCTTTGTGCATTGTTAAAACATTTGTACCAGATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAAt              <  2:548808/136‑1 (MQ=255)

                                                                                                                              tttGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGcc     <  2:494620/141‑1 (MQ=255)

                                                                                                                                tgtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCAc   >  1:309060/1‑141 (MQ=255)

                                                                                                                                 gtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCAcg  >  1:160001/1‑141 (MQ=255)

TATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACG  >  USA300TCH1516_ALE/1744231‑1744500

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A