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	4,352,880	G→A	99 (TAG→TAA)	ghoS →	antitoxin of GhoTS toxin‑antitoxin pair, endonuclease for ghoT mRNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,352,880	0	G	A	98.5%	211.8 / NA	67	99 (TAG→TAA)	ghoS	antitoxin of GhoTS toxin‑antitoxin pair, endonuclease for ghoT mRNA
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (26/40); total (26/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAGCCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTA  >  NC_000913/4352746‑4353009

ttCGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCag                                                                                                                               <  1:1053782/139‑1 (MQ=255)

ttCGCAATAACGACATAGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGAATTACTGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAGCCag                                                                                                                               <  1:75527/139‑1 (MQ=255)

 tCGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagg                                                                                                                              <  1:1045316/139‑1 (MQ=255)

  cGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  2:1161790/139‑1 (MQ=255)

  cGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:640629/139‑1 (MQ=255)

  cGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  2:708296/139‑1 (MQ=255)

  cGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:474151/139‑1 (MQ=255)

  cGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:1627/139‑1 (MQ=255)

  cGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:438636/139‑1 (MQ=255)

  cGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTGTACAAGTAACCagga                                                                                                                             <  1:698045/139‑1 (MQ=255)

         aCGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATaa                                                                                                                      >  2:1714986/1‑139 (MQ=255)

              aTCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  2:590958/127‑1 (MQ=255)

              aTCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             >  1:590958/1‑127 (MQ=255)

              aTCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAagaaga                                                                                                                 >  1:279672/1‑139 (MQ=255)

                  ttAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCag                                                                                                                               <  1:124050/121‑1 (MQ=255)

                  ttAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCag                                                                                                                               >  2:124050/1‑121 (MQ=255)

                    aGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagg                                                                                                                              >  1:624968/1‑120 (MQ=255)

                    aGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagg                                                                                                                              <  2:624968/120‑1 (MQ=255)

                        gCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATaaaaaa                                                                                                       <  1:143612/139‑1 (MQ=255)

                         cAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAAt                                                                                                      >  1:1752306/1‑139 (MQ=255)

                          aaGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:1391962/115‑1 (MQ=255)

                          aaGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             >  2:1391962/1‑115 (MQ=255)

                             tGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCa                                                                                                  <  1:611871/139‑1 (MQ=255)

                             tGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCa                                                                                                  <  2:592937/139‑1 (MQ=255)

                             tGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCa                                                                                                  <  1:1714986/139‑1 (MQ=255)

                               aaaTCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACt                                                                                                >  1:1371648/1‑139 (MQ=255)

                                                  gCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAAtt                                                                             >  1:494334/1‑139 (MQ=255)

                                                  gCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACCATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAAtt                                                                             >  1:1301041/1‑139 (MQ=255)

                                                            ttAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:904728/81‑1 (MQ=255)

                                                            ttAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             >  2:904728/1‑81 (MQ=255)

                                                            ttAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATaaaaaa                                                                                                       <  2:1492934/103‑1 (MQ=255)

                                                            ttAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATaaaaaa                                                                                                       >  1:1492934/1‑103 (MQ=255)

                                                            ttAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGa                                                                   <  2:1371648/139‑1 (MQ=255)

                                                            ttAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGa                                                                   <  1:1012957/139‑1 (MQ=255)

                                                            ttAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGa                                                                   <  2:279672/139‑1 (MQ=255)

                                                                  ttACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             >  1:482570/1‑75 (MQ=255)

                                                                  ttACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  2:482570/75‑1 (MQ=255)

                                                                  ttACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGgtg                                                             <  2:380780/139‑1 (MQ=255)

                                                                    aCCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGa                                                                   <  1:17843/131‑1 (MQ=255)

                                                                    aCCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGa                                                                   >  2:17843/1‑131 (MQ=255)

                                                                        gATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACa                                                       <  2:693041/139‑1 (MQ=255)

                                                                          tatTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGTACTATTCTCTAAAATATTAATTTTTTa                                                                        <  1:1072090/120‑1 (MQ=255)

                                                                          tatTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGACACTATTCTCTAAAATATTAATTTTTTa                                                                        >  2:1072090/1‑120 (MQ=255)

                                                                              gATTTTGACCTCAACATTATGACAGTTGATGACCATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCt                                                 <  2:1301041/139‑1 (MQ=255)

                                                                                ttttGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             >  2:1455550/1‑61 (MQ=255)

                                                                                ttttGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:1455550/61‑1 (MQ=255)

                                                                                   tGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             <  1:284788/58‑1 (MQ=255)

                                                                                   tGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCagga                                                                                                                             >  2:284788/1‑58 (MQ=255)

                                                                                   tGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTc                                            <  2:494334/139‑1 (MQ=255)

                                                                                                 tGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCa                                                                                                  <  2:138007/71‑1 (MQ=255)

                                                                                                 tGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCa                                                                                                  >  1:138007/1‑71 (MQ=255)

                                                                                                 tGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTAt                              >  2:1255262/1‑139 (MQ=255)

                                                                                                      gTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATaaaaaa                                                                                                       <  2:643405/61‑1 (MQ=255)

                                                                                                      gTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATaaaaaa                                                                                                       >  1:643405/1‑61 (MQ=255)

                                                                                                      gTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGgt                                                              >  2:95616/1‑102 (MQ=255)

                                                                                                      gTTGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGgt                                                              <  1:95616/102‑1 (MQ=255)

                                                                                                       ttGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGa                                                                   <  2:505563/96‑1 (MQ=255)

                                                                                                       ttGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGa                                                                   >  1:505563/1‑96 (MQ=255)

                                                                                                       ttGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTATCTcaca                        <  2:149257/139‑1 (MQ=255)

                                                                                                       ttGATGACTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTATCTcaca                        >  1:149257/1‑139 (MQ=255)

                                                                                                             aCTATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTATCTCACATGAGaa                  <  2:1752306/139‑1 (MQ=255)

                                                                                                               tATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTAtt                                                                                             >  2:1366456/1‑62 (MQ=255)

                                                                                                               tATTTCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTAtt                                                                                             <  1:1366456/62‑1 (MQ=255)

                                                                                                                   tCCGTCAGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAGAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAAcaca            <  1:1255262/139‑1 (MQ=255)

                                                                                                                         aGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGAt                                                                  >  2:431118/1‑79 (MQ=255)

                                                                                                                         aGTTTTACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGAt                                                                  <  1:431118/79‑1 (MQ=255)

                                                                                                                             ttACAAGTAACCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTa  >  2:1423903/1‑139 (MQ=255)

TTCGCAATAACGACATCGTTAGCCGCAAGTGAAATCGAAGATTTAATCAGGCTCAAATGCTTAGACTTACCGGATATTGATTTTGACCTCAACATTATGACAGTTGATGACTATTTCCGTCAGTTTTACAAGTAGCCAGGAAGGATAAGAAGAACATAAAAAATGGCACTATTCTCTAAAATATTAATTTTTTATGTGATTGGTGTGAACATATCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTA  >  NC_000913/4352746‑4353009

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A