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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,608,347 C→A 32.5% T85T (ACG→ACT)  nikR ← DNA‑binding transcriptional regulator, Ni‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,608,3470CA32.5% 169.2 / 90.7 138T85T (ACG→ACT) nikRDNA‑binding transcriptional regulator, Ni‑binding
Reads supporting (aligned to +/- strand):  ref base C (19/74);  new base A (24/21);  total (43/95)
Fisher's exact test for biased strand distribution p-value = 1.61e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

Only 100 of 138 total aligned reads displayed.

CGTCACCCATGTCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTC  >  minE/2608280‑2608406
                                                                   |                                                           
cGTCACCCATGTCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCg                                                            >  1:561949/1‑69 (MQ=255)
       cATGTCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGa                                                      >  1:482842/1‑68 (MQ=255)
           tCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGgag                                                 >  1:2110366/1‑69 (MQ=255)
           tCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGgag                                                 >  1:1403351/1‑69 (MQ=255)
             tccTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGagag                                               >  1:510737/2‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCgt                                          >  1:976270/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCgt                                          >  1:937469/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCg                                           >  1:672569/1‑68 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:1962500/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:2196958/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:2201567/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:1783126/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:1665106/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:1654351/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:114437/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:63967/1‑69 (MQ=255)
                  tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                          >  1:1259381/1‑69 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:560741/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:2410845/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:1987056/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:2060009/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:782643/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:657747/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:2345623/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:531742/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:2422476/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:2437349/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:2664431/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:2728845/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    >  1:2935058/1‑69 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:3199509/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:338830/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:371080/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:44578/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:1917526/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:152634/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:1874796/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:183659/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:1172553/69‑1 (MQ=255)
                        cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                    <  1:1083721/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:101448/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:195223/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:3282415/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:333752/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:2739746/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:429486/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:1415552/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:1590093/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:2066473/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:21343/69‑1 (MQ=255)
                          gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:216970/69‑1 (MQ=255)
                           cGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:765458/68‑1 (MQ=255)
                             aTTTCCAGACAGTCGTCGTTGTTGATGTTCACATGCAGCGTGGCGACGGAGAGGTCGTGGttat                                    <  1:635422/64‑1 (MQ=255)
                                     aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                       <  1:1541643/69‑1 (MQ=255)
                                     aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                       <  1:1034208/69‑1 (MQ=255)
                                     aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                       <  1:1994753/69‑1 (MQ=255)
                                     aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                       <  1:3434987/69‑1 (MQ=255)
                                     aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                       <  1:2136495/69‑1 (MQ=255)
                                        gtcgtcGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGAc                    <  1:888066/69‑1 (MQ=255)
                                        gtcgtcGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGAc                    <  1:387020/69‑1 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:1490485/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:85565/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:912637/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:149822/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:808701/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:3226086/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:6961/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:2083835/1‑69 (MQ=255)
                                           gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                 >  1:2818169/1‑69 (MQ=255)
                                                 gTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggct           >  1:2281802/1‑69 (MQ=255)
                                                 gTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggct           >  1:116872/1‑69 (MQ=255)
                                                   tGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggctg          >  1:3143892/1‑68 (MQ=255)
                                                   tGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggctg          >  1:2969121/1‑68 (MQ=255)
                                                    gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                       <  1:128624/38‑1 (MQ=255)
                                                    gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                       <  1:17314/38‑1 (MQ=255)
                                                    gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                       <  1:236473/38‑1 (MQ=255)
                                                    gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                       <  1:2567313/38‑1 (MQ=255)
                                                    gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                       <  1:1546594/38‑1 (MQ=255)
                                                    gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                       <  1:1465645/38‑1 (MQ=255)
                                                    gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                       <  1:2801272/38‑1 (MQ=255)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCTTGGTGATGATGCTTGGTGGAGACa                   <  1:1260820/54‑1 (MQ=255)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:3432073/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:19231/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:973421/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:311943/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:1831189/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:2201790/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:3357307/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:464601/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:1619454/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:2799138/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:2725514/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:2620510/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:1502119/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:1349078/54‑1 (MQ=37)
                                                        tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:1406988/54‑1 (MQ=37)
                                                         gCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                   <  1:1036915/53‑1 (MQ=25)
                                                          cacaTGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTc  >  1:1074587/1‑69 (MQ=255)
                                                          cacaTGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTc  >  1:945277/1‑69 (MQ=255)
                                                           acaTGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                  <  1:507178/36‑1 (MQ=255)
                                                                   |                                                           
CGTCACCCATGTCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTC  >  minE/2608280‑2608406

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