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
A15 F18 I40 R1	11	54.2	1757834	98.4%	1729708	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	2,870,339	G→A	G134S (GGC→AGC)	iap →	aminopeptidase in alkaline phosphatase isozyme conversion

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,870,339	0	G	A	96.3%	156.9 / ‑4.5	54	G134S (GGC→AGC)	iap	aminopeptidase in alkaline phosphatase isozyme conversion
Reads supporting (aligned to +/- strand): ref base G (0/2); new base A (25/27); total (25/29)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CGCGATAATCGTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCGGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTAGGCGC  >  CP009273/2870195‑2870484

cgcgATAATCGTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTcagcgg                                                                                                                                               >  1:329511/1‑149 (MQ=255)

  cgATAATCGTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGc                                                                                                                                             >  1:294247/1‑149 (MQ=255)

          gTAAGCGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGGAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTg                                                                                                                                           <  2:379498/143‑1 (MQ=255)

          gTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCTATGCTGACGCCGATGCCAATCTCAGCGGGCTg                                                                                                                                           <  2:379743/143‑1 (MQ=255)

          gTAACAGCTGGCATAACGTGACGGGAAGTACGGGGATTGCCGCTCATGAAGGCAAAGCGGCGCAGCAGAGCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTg                                                                                                                                           <  2:6317/143‑1 (MQ=255)

            aaGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGAc                                                                                                                                         <  2:358155/143‑1 (MQ=255)

                    gCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACCAGGAATgg                                                                                                                           >  1:50261/1‑149 (MQ=255)

                    gCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAg                                                                                                                                 >  2:158799/1‑143 (MQ=255)

                    gCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATgg                                                                                                                           >  1:63195/1‑149 (MQ=255)

                     cATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGga                                                                                                                          <  1:152569/149‑1 (MQ=255)

                      aTAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGgat                                                                                                                         >  1:863911/1‑149 (MQ=255)

                      aTAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGAGCATCAGTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAACGGGCTGACGTTCCACGGa                                                                                                                               >  2:150657/1‑143 (MQ=255)

                       tAACGTGACGGGAAGTACGGTGATGGCCGCTCATGCAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGaa                                                                                                                              <  2:478062/143‑1 (MQ=255)

                         aCGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATg                                                                                                                            <  2:793637/143‑1 (MQ=255)

                              aCGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGgatga                                                                                                                       <  2:90287/143‑1 (MQ=255)

                               cGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAAcgcc                                                                                                                <  1:543901/149‑1 (MQ=255)

                                  gAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAAc                                                                                                                   >  2:690176/1‑143 (MQ=255)

                                           tGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCGGACGTTACAAGGGATGGATGATAACGCCGCAGGt                                                                                                          >  2:169709/1‑143 (MQ=255)

                                               tGCCGCTCATGAAGGCCAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAg                                                                                                      <  2:466324/143‑1 (MQ=255)

                                                         gAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCt                                                                                            >  2:830712/1‑143 (MQ=255)

                                                         gAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGAAGATAACGCCGCAGGTTTAGGTGTCATGCTGGAAtt                                                                                      >  1:734001/1‑149 (MQ=255)

                                                         gAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCAGATGCCAATCTCAGCGGGCTGACGATACAAGGAATGGATGATAACGCCGCAGGTTTAGGGGTCGTGCt                                                                                            >  2:155348/1‑143 (MQ=255)

                                                           aGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCAGCAGGTTTAGGTGTCATGCTgg                                                                                          >  2:758616/1‑143 (MQ=255)

                                                            ggCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGc                                                                                   >  1:353984/1‑149 (MQ=255)

                                                             gCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCa                                                                                  <  1:898054/149‑1 (MQ=255)

                                                              cAAAGCTCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCGGCGGGCTGACCTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAg                                                                                 <  1:181175/149‑1 (MQ=255)

                                                              cAAAGCGCAGCAGCAGACCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGGGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAAt                                                                                       <  2:284639/143‑1 (MQ=255)

                                                              aaacgcgcCGCAGCAGATCATCAATATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCGGCGGGCTGACGTTACCAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAg                                                                                 <  1:762277/145‑1 (MQ=255)

                                                                 aGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGCTAACGCCGCAGGTTTAGGTGTCATGCTGGAATTgg                                                                                    <  2:459361/143‑1 (MQ=255)

                                                                     ccgcAGAAGATCATACTTATGGCGCATTTGGATACTTACTCCCCGCTGAGCGATGCTGAGGCCGGTGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTAATGCTGGAATTGGCAGa                                                                                >  2:699880/1‑143 (MQ=255)

                                                                     cagcagcaGATAATCATTATGGCGCATCTGTATACTTACGCCCCGCTTAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGa                                                                                >  2:699874/3‑143 (MQ=255)

                                                                                 atcacgaTGGCGCATCTGGATACTTACGCACCGCTGGGCGATGCTGACGCCGATGCCAATCTCAGCGGGCCGACCTTACCAGGAATGGATGATAACGCCGCAAGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGaaaaa                                                                    <  2:810708/137‑1 (MQ=255)

                                                                                 accatTATGGCGCAGCTGGATACTTACGCCCCGCTGAGCGAGGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGaaaaa                                                                    <  2:486525/141‑1 (MQ=255)

                                                                                  tcatTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAAt                                                                   <  2:223837/143‑1 (MQ=255)

                                                                                      tATGGCGCATCTGGATACTTACGCCCCGCTGGGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTAAAAGGAATGGATGATAACGCCGCAGGTTTGGGGGGCATGATGGAATTGGCAGAACGCCTGAAAAATACGc                                                               <  2:75668/143‑1 (MQ=255)

                                                                                       aTGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGa                                                        <  1:174427/149‑1 (MQ=255)

                                                                                          gcgcATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAAGGCCTGAAAAATTCGCCTAc                                                           <  2:811975/143‑1 (MQ=255)

                                                                                            gcATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATg                                                   <  1:755508/149‑1 (MQ=255)

                                                                                            ccATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAACCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCg                                                         <  2:159118/142‑1 (MQ=255)

                                                                                                cTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAAGAAGCCTACCGAgga                                                     >  2:104314/1‑141 (MQ=255)

                                                                                                  ggATACTTACGCCCCGCTGAGCGATGCTGGCGCGGAGGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTc                                             >  1:906141/1‑149 (MQ=255)

                                                                                                   gATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATgg                                                  <  2:698583/143‑1 (MQ=255)

                                                                                                        ttACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAGTGGATGATAACGCCGCAGGGTTAGGTGTCATGCTGGAATTGGCAGAACGCCGGAGAAATGCGGCTCCCGGGTCTGGTAttg                                             >  2:424717/1‑142 (MQ=255)

                                                                                                                 gccgcacaacgcctaCGCCGACGCCCATCCCATCGGGCGGACGTTACAAGGAATGCATGATAACCCCGCAGGTTTAGGTGTCATCCTGGAATTGGCAGAACGCCTGAAAAACACGCCTACCGAGTATGGTATTCGATTTGTgg                                    <  2:790488/129‑1 (MQ=255)

                                                                                                                 gCTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTgg                                    <  2:675631/143‑1 (MQ=255)

                                                                                                                  cTGAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGc                                   >  2:328382/1‑143 (MQ=255)

                                                                                                                    gAGCGATGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAgcg                           <  1:9911/149‑1 (MQ=255)

                                                                                                                       cGATGGCGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATCATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTCTGGTTTTCGATTTGTGGCGACCa                              <  2:508363/143‑1 (MQ=255)

                                                                                                                          tGCTGACGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAag                     <  1:550426/149‑1 (MQ=255)

                                                                                                                               aCGCCGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGAGGACATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGAATGGTATTCGCGTTGTGGCGACCAGCGGCGaa                      >  2:193642/1‑143 (MQ=255)

                                                                                                                                   cGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGa            >  1:508887/1‑149 (MQ=255)

                                                                                                                                   cGATGCCAATCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTAGCGACCAACGGCGAAGAGGAAGGGa            >  1:562315/1‑149 (MQ=255)

                                                                                                                                    gATGCCAATCTGAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGAAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGCGTCGTGGCGACCAGCGGCGAAGGGGa                 >  2:490438/1‑143 (MQ=255)

                                                                                                                                           aTCTCAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTAGgc    >  1:255843/1‑149 (MQ=255)

                                                                                                                                             ctcAGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTAGgcgc  >  1:162822/1‑149 (MQ=255)

CGCGATAATCGTAAGAGCTGGCATAACGTGACGGGAAGTACGGTGATTGCCGCTCATGAAGGCAAAGCGCCGCAGCAGATCATCATTATGGCGCATCTGGATACTTACGCCCCGCTGAGCGATGCTGACGCCGATGCCAATCTCGGCGGGCTGACGTTACAAGGAATGGATGATAACGCCGCAGGTTTAGGTGTCATGCTGGAATTGGCAGAACGCCTGAAAAATACGCCTACCGAGTATGGTATTCGATTTGTGGCGACCAGCGGCGAAGAGGAAGGGAAATTAGGCGC  >  CP009273/2870195‑2870484

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