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	2,608,356	G→T	31.4%	S82S (TCC→TCA)	nikR ←	DNA‑binding transcriptional regulator, Ni‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,608,356	0	G	T	31.4%	180.8 / 88.5	143	S82S (TCC→TCA)	nikR	DNA‑binding transcriptional regulator, Ni‑binding
Reads supporting (aligned to +/- strand): ref base G (17/81); new base T (24/21); total (41/102)
Fisher's exact test for biased strand distribution p-value = 2.03e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.19e-01

Only 100 of 143 total aligned reads displayed.

TCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTCGCGTTTTTCGTGTTCA  >  minE/2608291‑2608422

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)

       tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                                          >  1:1665106/1‑69 (MQ=255)

       tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                                          >  1:1654351/1‑69 (MQ=255)

       tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                                          >  1:1783126/1‑69 (MQ=255)

       tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                                          >  1:1259381/1‑69 (MQ=255)

       tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                                          >  1:2371917/1‑69 (MQ=255)

       tCAACACGGCGATTTCCAGACAGTCGTCGTGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCgt                                                          >  1:2201567/1‑69 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:3178656/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:338830/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:2422476/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:3328935/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:183659/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:1917526/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:3199509/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:2345623/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:1987056/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    >  1:2935058/1‑69 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:2060009/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:2437349/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:2722017/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:2728845/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:2198654/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:1083721/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:90283/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:344498/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:782643/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:1172553/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:152634/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:657747/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:560741/69‑1 (MQ=255)

             cGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgat                                                    <  1:1337538/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:2066473/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:101448/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:1235241/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:216970/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:2739746/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:653551/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:1415552/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:195223/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:3282415/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:429486/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:1590093/69‑1 (MQ=255)

               gCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGtgatga                                                  <  1:333752/69‑1 (MQ=255)

                  aTTTCCAGACAGTCGTCGTTGTTGATGTTCACATGCAGCGTGGCGACGGAGAGGTCGTGGttat                                                    <  1:635422/64‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATTCTGGGTGga                                       <  1:2103093/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:1034208/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:53113/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:3434987/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:1994753/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:1550741/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:1834952/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:1541643/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGga                                       <  1:2136495/69‑1 (MQ=255)

                          aCAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTCGGTGga                                       <  1:440036/69‑1 (MQ=255)

                             gtcgtcGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGAc                                    <  1:387020/69‑1 (MQ=255)

                             gtcgtcGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGAc                                    <  1:888066/69‑1 (MQ=255)

                                gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                                 >  1:808701/1‑69 (MQ=255)

                                gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                                 >  1:1759075/1‑69 (MQ=255)

                                gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                                 >  1:6961/1‑69 (MQ=255)

                                gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                                 >  1:825004/1‑69 (MQ=255)

                                gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                                 >  1:2818169/1‑69 (MQ=255)

                                gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                                 >  1:149822/1‑69 (MQ=255)

                                gtcgtGATTAATGTGCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACAAt                                 >  1:1490373/1‑69 (MQ=255)

                                      gTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggct                           >  1:47114/1‑69 (MQ=255)

                                      gTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggct                           >  1:1918544/1‑69 (MQ=255)

                                      gTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggct                           >  1:2281802/1‑69 (MQ=255)

                                        tGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggctg                          >  1:2969121/1‑68 (MQ=255)

                                        tGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCggctg                          >  1:2138068/1‑68 (MQ=255)

                                         gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                                       <  1:236473/38‑1 (MQ=255)

                                         gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                                       <  1:128624/38‑1 (MQ=255)

                                         gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                                       <  1:1465645/38‑1 (MQ=255)

                                         gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                                       <  1:3410160/38‑1 (MQ=255)

                                         gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                                       <  1:2567313/38‑1 (MQ=255)

                                         gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                                       <  1:3018197/38‑1 (MQ=255)

                                         gATGTGCACATGCAGCGTGGCGACGGAGAGGTCgtggt                                                       <  1:2802021/38‑1 (MQ=255)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:2799138/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:1163407/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:744303/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:2620510/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:1406988/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:2725514/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:603000/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:1619454/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:1502119/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:464601/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:311943/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:973421/54‑1 (MQ=37)

                                             tgCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:1831189/54‑1 (MQ=37)

                                              gCACATGCAGAGTAGCAACTGAGAGATCGTGGTGATGATGCTGGGTGGAGACa                                   <  1:1036915/53‑1 (MQ=25)

                                               cacaTGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTc                  >  1:1980633/1‑69 (MQ=255)

                                               cacaTGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTc                  >  1:1074587/1‑69 (MQ=255)

                                               cacaTGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTc                  >  1:945277/1‑69 (MQ=255)

                                                               aCGGAGAGGTCGTGGTGATGATGCTGGGTGTAGACAATGCGGCTGGCTAAGTCGCGTTTTTCGTGTTCa  <  1:2312732/69‑1 (MQ=255)

                                                               aCGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTCGCGTTTTTCGTGTTCa  <  1:1944925/69‑1 (MQ=255)

                                                               aCGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTCGCGTTTTTCGTGTTCa  <  1:11517/69‑1 (MQ=255)

                                                               aCGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTCGCGTTTTTCGTGTTCa  <  1:3139142/69‑1 (MQ=255)

TCACCTTTCAACACGGCGATTTCCAGACAGTCGTCGTGGTTGATGTGCACATGCAGCGTGGCGACGGAGAGGTCGTGGTGATGATGCTGGGTGGAGACAATGCGGCTGGCTAAGTCGCGTTTTTCGTGTTCA  >  minE/2608291‑2608422

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