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 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,946,407	G→A	78.4%	intergenic (‑121/+121)	fecI ← / ← dnaC	RNA polymerase, sigma 19 factor/DNA biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,946,407	0	G	A	78.4%	207.3 / 54.0	111	intergenic (‑121/+121)	fecI/dnaC	RNA polymerase, sigma 19 factor/DNA biosynthesis protein
Reads supporting (aligned to +/- strand): ref base G (16/8); new base A (43/44); total (59/52)
Fisher's exact test for biased strand distribution p-value = 1.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01

Only 100 of 118 total aligned reads displayed.

GTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATG  >  minE/2946338‑2946474

gTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGtgttgt                                                                    <  1:3927496/71‑1 (MQ=255)

gTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGtgttg                                                                     >  1:4412795/1‑70 (MQ=255)

   aTCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAag                                                                 >  1:5059128/1‑71 (MQ=255)

    tCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAag                                                                 <  1:3649818/70‑1 (MQ=255)

      aTTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggt                                                               <  1:2497535/70‑1 (MQ=255)

      aTTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAagg                                                                >  1:3662092/1‑69 (MQ=255)

      aTTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAagg                                                                >  1:2398297/1‑69 (MQ=255)

       ttACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAaggtag                                                             <  1:5193877/71‑1 (MQ=255)

           aaTTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGtat                                                         <  1:2939083/71‑1 (MQ=255)

                 aaaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaaa                                                     <  1:1830628/69‑1 (MQ=255)

                 aaaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATg                                                   <  1:2912234/71‑1 (MQ=255)

                  aataatATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaa                                                       <  1:1943724/66‑1 (MQ=255)

                  aaTAAAATTGTTTCCAATAGTCATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATgg                                                  <  1:2178097/71‑1 (MQ=255)

                  aaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATgg                                                  <  1:5528218/71‑1 (MQ=255)

                  aaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAag                                                                 >  1:3313605/1‑56 (MQ=255)

                  aaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGtata                                                        <  1:610227/65‑1 (MQ=255)

                  aaTAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATgg                                                  <  1:1053195/71‑1 (MQ=255)

                    tAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGa                                                >  1:2432883/1‑71 (MQ=255)

                      aaaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggta                                                              <  1:887936/55‑1 (MQ=255)

                      aaaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggta                                                              <  1:3904877/55‑1 (MQ=255)

                      aaaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggta                                                              <  1:5533329/55‑1 (MQ=255)

                       aaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATg                                                   >  1:3148511/1‑65 (MQ=255)

                       aaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAAt                                                    <  1:1654502/64‑1 (MQ=255)

                       aaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAAt                                                    <  1:2159547/64‑1 (MQ=255)

                       aaTTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAAt                                                    <  1:3970740/64‑1 (MQ=255)

                         ttGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAag                                                                 >  1:4868027/1‑49 (MQ=255)

                         ttGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATaaa                                                      >  1:196488/1‑60 (MQ=255)

                         ttGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATaaa                                                      >  1:1480459/1‑60 (MQ=255)

                           gTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATg                                                   >  1:5486237/1‑61 (MQ=255)

                           gTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATg                                                   >  1:4527271/1‑61 (MQ=255)

                           gTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGa                                                >  1:676627/1‑64 (MQ=255)

                            tttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATgg                                                  <  1:3335845/61‑1 (MQ=255)

                            tttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGcc                                         <  1:1741337/70‑1 (MQ=255)

                             ttCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCct                                        >  1:4360146/1‑70 (MQ=255)

                              tCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAaggt                                                               >  1:4140920/1‑46 (MQ=255)

                                cAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGa                                            >  1:3880672/1‑63 (MQ=255)

                                cAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATg                                              >  1:4091454/1‑61 (MQ=255)

                                cAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGc                                    <  1:2524049/71‑1 (MQ=255)

                                cAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGc                                    >  1:5614409/1‑71 (MQ=255)

                                cAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGc                                    <  1:1260887/71‑1 (MQ=255)

                                cAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGc                                    >  1:3644090/1‑71 (MQ=255)

                                 aaTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCt                                   <  1:4053747/71‑1 (MQ=255)

                                  aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCtt                                  >  1:4616064/1‑71 (MQ=255)

                                  aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCtt                                  >  1:3176177/1‑71 (MQ=255)

                                  aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCtt                                  >  1:4203284/1‑71 (MQ=255)

                                  aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaa                                                      <  1:751446/51‑1 (MQ=255)

                                  aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaa                                                      <  1:1131929/51‑1 (MQ=255)

                                  aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaa                                                      <  1:3195003/51‑1 (MQ=255)

                                  aTAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaa                                                      <  1:2232489/51‑1 (MQ=255)

                                   tAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAag                                                                 >  1:5692346/1‑39 (MQ=255)

                                   tAGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaa                                                      <  1:5173233/50‑1 (MQ=255)

                                    aGACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaaa                                                     >  1:2375826/1‑50 (MQ=255)

                                     gACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATgg                                                  <  1:2851989/52‑1 (MQ=255)

                                     gACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGa                                            >  1:5388260/1‑58 (MQ=255)

                                     gACATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTACGTATaa                                                       <  1:732130/47‑1 (MQ=255)

                                      aCATTTTTAACATGTTGTTTTTCTAAGTGTTGTAaggt                                                               <  1:120539/38‑1 (MQ=255)

                                       cATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaaa                                                     >  1:1210148/1‑47 (MQ=255)

                                       cATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaaa                                                     >  1:2800386/1‑47 (MQ=255)

                                       cATTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTgg                              <  1:5007717/70‑1 (MQ=255)

                                        aTTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCa                            >  1:5408/1‑71 (MQ=255)

                                        aTTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCa                            >  1:3427589/1‑71 (MQ=255)

                                        aTTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGc                                          >  1:3388612/1‑57 (MQ=255)

                                        aTTTTTAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCa                            >  1:2576850/1‑71 (MQ=255)

                                         tttttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGtat                                                         <  1:1297479/41‑1 (MQ=255)

                                         tttttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGtat                                                         <  1:5120476/41‑1 (MQ=255)

                                         tttttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGtat                                                         <  1:1671327/41‑1 (MQ=255)

                                         tttttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATaaaa                                                     <  1:2140003/45‑1 (MQ=255)

                                          ttttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtg                          >  1:2116373/1‑71 (MQ=255)

                                           tttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGa                                                >  1:5128605/1‑48 (MQ=255)

                                           tttAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTg                                     >  1:2885880/1‑59 (MQ=255)

                                           tttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATg                                                   >  1:1735250/1‑45 (MQ=255)

                                           tttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATg                                                   >  1:241957/1‑45 (MQ=255)

                                            ttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtgt                         <  1:2674206/70‑1 (MQ=255)

                                            ttAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtgt                         <  1:563415/70‑1 (MQ=255)

                                             tAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCa                            >  1:1433359/1‑66 (MQ=255)

                                             tAACATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATgtgt                       >  1:3830289/1‑71 (MQ=255)

                                               aCATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCg                     >  1:162154/1‑71 (MQ=255)

                                               aCATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCct                                        >  1:5344837/1‑52 (MQ=255)

                                               aCATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGc                                    >  1:765015/1‑56 (MQ=255)

                                                cATGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCgg                    >  1:1454637/1‑71 (MQ=255)

                                                 aTGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGt                   <  1:2190638/71‑1 (MQ=255)

                                                 aTGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGt                   <  1:2738028/71‑1 (MQ=255)

                                                 aTGTTGTTTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGt                   <  1:5515239/71‑1 (MQ=255)

                                                    ttgttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAg                <  1:4502009/71‑1 (MQ=255)

                                                     tgttTTTCTAAGTGTTATAAGGTAGGTATAAAATGTGATgg                                             >  1:46678/1‑41 (MQ=255)

                                                     tgttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAg                >  1:1269848/1‑70 (MQ=255)

                                                     tgttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAg                >  1:1969940/1‑70 (MQ=255)

                                                      gttTTTCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGaa              >  1:3519701/1‑71 (MQ=255)

                                                       tttttCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCAtg                          >  1:4748484/1‑58 (MQ=255)

                                                        ttttCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAAt             >  1:1348751/1‑70 (MQ=255)

                                                        ttttCTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAAt             >  1:2844351/1‑70 (MQ=255)

                                                         tttCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGa           >  1:3645019/1‑71 (MQ=255)

                                                            cTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACt         <  1:3910347/70‑1 (MQ=255)

                                                            cTAAGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACt         <  1:1578711/70‑1 (MQ=255)

                                                               aGTGTTATAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCat      >  1:541494/1‑70 (MQ=255)

                                                                 tgttatAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTg                               >  1:4057233/1‑43 (MQ=255)

                                                                 tgttatAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTg                               >  1:1910848/1‑43 (MQ=255)

                                                                 tgttatAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCatgat   <  1:1298/71‑1 (MQ=255)

                                                                  gttatAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCatgatg  >  1:5027107/1‑71 (MQ=255)

                                                                   ttgtAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGGCAg                <  1:564302/56‑1 (MQ=255)

GTTATCATTACAATTGGAAATAAAATTGTTTCCAATAGACATTTTTAACATGTTGTTTTTCTAAGTGTTGTAAGGTAGGTATAAAATGGGATGGAGCCTCTGCTTCTGGCATGTGTCGGTCAGAATGACTCATGATG  >  minE/2946338‑2946474

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A