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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,439,816	G→A	18.6%	D162D (GAC→GAT) ‡	ompC ←	outer membrane porin protein C

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,439,816	0	G	A	18.6%	294.1 / 54.8	129	D162D (GAC→GAT) ‡	ompC	outer membrane porin protein C
Reads supporting (aligned to +/- strand): ref base G (66/39); new base A (10/14); total (76/53)
Fisher's exact test for biased strand distribution p-value = 6.81e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.08e-01

Only 100 of 129 total aligned reads displayed.

CACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTG  >  minE/1439749‑1439885

cACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTc                                                                     >  1:2167676/1‑70 (MQ=255)

  cTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  >  1:744548/1‑71 (MQ=255)

  cTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  >  1:1362640/1‑71 (MQ=255)

   tAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  >  1:2655663/1‑70 (MQ=255)

         aGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGAcc                                                            >  1:533000/1‑70 (MQ=255)

          gCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCga                                                          <  1:3173951/71‑1 (MQ=255)

           ccTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCg                                                           >  1:1339562/1‑69 (MQ=255)

               cacaAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:3147482/1‑71 (MQ=255)

               cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaagaa                                                      <  1:3148605/70‑1 (MQ=255)

               cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaaga                                                       <  1:1892107/69‑1 (MQ=255)

               cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:1319326/1‑71 (MQ=255)

               cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:1986726/1‑71 (MQ=255)

               cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:2249199/1‑71 (MQ=255)

               cACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag                                                     >  1:2077659/1‑71 (MQ=255)

                 ccAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc                                                   <  1:2850079/71‑1 (MQ=255)

                  cAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCa                                                  <  1:3281883/71‑1 (MQ=255)

                  cAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCa                                                  <  1:1939185/71‑1 (MQ=255)

                      tGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgtgt                                              <  1:134798/71‑1 (MQ=255)

                      tGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgtgt                                              <  1:1767127/71‑1 (MQ=255)

                         gTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTa                                            >  1:3070716/1‑70 (MQ=255)

                         gTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTAc                                           >  1:2273931/1‑71 (MQ=255)

                            gCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg                                         >  1:2088991/1‑70 (MQ=255)

                             tcGTTGTTACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACga                                         >  1:3865664/2‑68 (MQ=2)

                              cGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGt                                        <  1:3047435/69‑1 (MQ=255)

                              cGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAg                                      >  1:629630/1‑71 (MQ=255)

                              cGTTGTTACCTTGATACTGCACCGCGAAGTTCAGACAATTTACCAGACCGAAGAAATCAGTATTACgat                                        >  1:3357153/1‑67 (MQ=255)

                               gTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAgg                                     >  1:2133154/1‑71 (MQ=255)

                               gTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAgg                                     >  1:2364191/1‑71 (MQ=255)

                                tttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAAc                                                                  <  1:82039/41‑1 (MQ=255)

                                tttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGt                                        <  1:2949539/67‑1 (MQ=255)

                                tttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGt                                    >  1:1662705/1‑71 (MQ=255)

                                 ttttACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgtgt                                              >  1:2405916/1‑60 (MQ=255)

                                  gttACCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTc                                   <  1:2924173/69‑1 (MQ=255)

                                    tACCCTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgc                                 <  1:2593206/70‑1 (MQ=255)

                                     aCCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTcgcg                                <  1:1926335/70‑1 (MQ=255)

                                     aCCTTGATACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTcgcg                                <  1:3891873/70‑1 (MQ=255)

                                     aCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGt                                        <  1:1806140/62‑1 (MQ=255)

                                      cccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcgcg                                >  1:202365/1‑69 (MQ=255)

                                      cccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcgcg                                >  1:1247060/1‑69 (MQ=255)

                                      cccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcgcg                                <  1:2765595/69‑1 (MQ=255)

                                      cccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGa                               <  1:1979738/70‑1 (MQ=255)

                                      cccTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgcaac                              <  1:1605507/71‑4 (MQ=255)

                                      cccTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgcaac                              <  1:2843971/71‑4 (MQ=255)

                                      cccTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgcaa                               <  1:3432106/70‑3 (MQ=255)

                                      cccTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgcaa                               <  1:212156/70‑3 (MQ=255)

                                      cccTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGTtgca                                <  1:3448962/69‑2 (MQ=255)

                                       ccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTATGGTAGGTCGCGAAg                             <  1:541593/71‑1 (MQ=255)

                                       ccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGt                                        >  1:320875/1‑60 (MQ=255)

                                       ccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGt                                        >  1:1132752/1‑60 (MQ=255)

                                       ccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAg                             <  1:3639299/71‑1 (MQ=255)

                                       ccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAg                             <  1:3569742/71‑1 (MQ=255)

                                       ccTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAg                             <  1:2413742/71‑1 (MQ=255)

                                       ccTGATATTGCAAAGCAAAGTTCAAGCCATCGACCTAACCAAAGAAGCCATTGTTACGGTAGGt                                    <  1:2829234/64‑1 (MQ=255)

                                         tgatACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTCGCGACGc                            >  1:2967278/4‑70 (MQ=9)

                                         tGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGcc                           >  1:3453501/1‑71 (MQ=255)

                                         tGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGcc                           >  1:1207240/1‑71 (MQ=255)

                                          gatACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTCGCGACGcca                          >  1:2334103/3‑70 (MQ=255)

                                           gTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAg                             >  1:2475107/1‑67 (MQ=255)

                                           gTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         >  1:3323222/1‑71 (MQ=255)

                                           gTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         >  1:277325/1‑71 (MQ=255)

                                           gTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         <  1:2767405/71‑1 (MQ=255)

                                           atACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTCGCGACGcca                          <  1:956235/69‑2 (MQ=255)

                                           atACTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTCGCGACGcca                          <  1:2362503/69‑2 (MQ=255)

                                             aCTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTCGCGACGCCAttg                       >  1:1549251/1‑70 (MQ=255)

                                             aCTGCACCGCGAAGTTCAGACCATTTACCAGACCGAAGAAATCAGTATTACGATAAGTCGCGACGCCAttg                       >  1:1124359/1‑70 (MQ=255)

                                              cTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaag                                                        <  1:3823167/37‑1 (MQ=255)

                                              cTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTa                                            >  1:3378310/1‑49 (MQ=255)

                                              cTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTAc                      <  1:1444877/71‑1 (MQ=255)

                                                 aaCAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCAc                   >  1:3771385/1‑71 (MQ=255)

                                                  aCAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACg                  <  1:2900722/71‑1 (MQ=255)

                                                   cAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCg                          >  1:3010504/1‑62 (MQ=255)

                                                     gCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTa                                            <  1:2088577/42‑1 (MQ=255)

                                                      cgaaGTTCAGACCATTTACCAGACCGAAGAAATCAGTAtt                                             <  1:876569/38‑1 (MQ=12)

                                                       aaaGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACgctgct             >  1:288432/1‑71 (MQ=255)

                                                       aaaGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACgctgct             >  1:459440/1‑71 (MQ=255)

                                                        aaGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgt                                                <  1:670203/35‑1 (MQ=255)

                                                        aaGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg                                         >  1:1433708/1‑42 (MQ=255)

                                                         aGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGctgctg            >  1:3007767/1‑70 (MQ=255)

                                                          gTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTa                       >  1:1529600/1‑58 (MQ=255)

                                                          gTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTAc                      >  1:2840793/1‑59 (MQ=255)

                                                          gTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCtgctgc           >  1:3128980/1‑70 (MQ=255)

                                                          gTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCa          <  1:3667624/71‑1 (MQ=255)

                                                          gTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCa          <  1:1545053/71‑1 (MQ=255)

                                                          gTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCa          >  1:1738353/1‑71 (MQ=255)

                                                             cAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGt                         >  1:3801564/1‑53 (MQ=255)

                                                             cAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATg        <  1:1066064/70‑1 (MQ=255)

                                                             cAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATg        >  1:2113501/1‑70 (MQ=255)

                                                             cAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTAACACGCTGCTGCATg        <  1:2090055/70‑1 (MQ=255)

                                                             agggCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGCTCGCGAAGCCGt                         >  1:847743/3‑53 (MQ=255)

                                                              aGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcg                                  >  1:419455/1‑43 (MQ=255)

                                                              aGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcg                                  >  1:2600455/1‑43 (MQ=255)

                                                               ggCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAg     >  1:649939/1‑71 (MQ=255)

                                                               ggCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAg     <  1:2603702/71‑1 (MQ=255)

                                                                gCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTcgcg                                <  1:1387196/43‑1 (MQ=255)

                                                                 ccGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTTCATGAAGtt   <  1:1082344/71‑1 (MQ=255)

                                                                  cGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCa                    >  1:3421887/1‑53 (MQ=255)

                                                                  cGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTg  >  1:1218480/1‑71 (MQ=255)

                                                                  cGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTg  >  1:2465204/1‑71 (MQ=255)

                                                                  cGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTg  <  1:3459522/71‑1 (MQ=255)

                                                                  cGTCAACCAGACCGAAGAAGCCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTg  >  1:401130/1‑71 (MQ=255)

CACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGTCGCGAAGCCGTTACCACGCTGCTGCATGAAGTTG  >  minE/1439749‑1439885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A