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	2,605,106	A→G	34.5%	L106L (TTG→CTG)	uspA ←	universal stress global response regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,605,106	0	A	G	34.5%	75.9 / 62.5	108	L106L (TTG→CTG)	uspA	universal stress global response regulator
Reads supporting (aligned to +/- strand): ref base A (25/45); new base G (12/25); total (37/71)
Fisher's exact test for biased strand distribution p-value = 8.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

Only 100 of 111 total aligned reads displayed.

TGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTT  >  minE/2605048‑2605174

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:2386069/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:1736703/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:1776739/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:1637523/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:667248/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:2331444/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:1011303/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:3302995/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:3220038/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:2770828/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:1119382/69‑1 (MQ=255)

tGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:3008720/69‑1 (MQ=255)

 gACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:2074836/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:3392724/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:3022584/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:2228548/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:504189/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:3087194/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:1809/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:3062436/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:1773828/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:756409/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:1070033/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:1169904/68‑1 (MQ=255)

         gAAGACATCAGTTTGCTCCAGAAGTACTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCtt                                                    <  1:3243295/68‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:946663/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:2622096/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:867040/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:3325190/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:2559192/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:3357955/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:1278447/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:2415433/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:693683/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:3113529/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:340692/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:373455/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:501948/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:111617/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:1791332/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:1973104/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:1816452/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:512517/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:1905821/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:1857531/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:528522/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTATTGAtt                                                <  1:2093242/69‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCg                                                            <  1:2621238/57‑1 (MQ=255)

            gACATCAGTTTGCTCCAGAAGTCCTCGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:2779034/69‑1 (MQ=255)

             aCATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCACATCCATATCGTATTTCTTGAtt                                                <  1:228120/68‑1 (MQ=255)

             aCATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTg                                               <  1:499459/69‑1 (MQ=255)

             aCATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTg                                               <  1:1777045/69‑1 (MQ=255)

             aCATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTg                                               <  1:1661226/69‑1 (MQ=255)

             aCATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTg                                               <  1:2046991/69‑1 (MQ=255)

             aCATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTg                                               <  1:1517150/69‑1 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTg                                               >  1:2304598/1‑68 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:941221/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:3081182/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:55302/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:3240645/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:2404073/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:453706/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:472135/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:581131/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:16125/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:2003611/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGc                                              >  1:1724155/1‑69 (MQ=255)

              cATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAAT‑CATATAGTAatt                                                       >  1:1442815/1‑59 (MQ=255)

              cATCAGTTTGATACAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTg                                               >  1:243748/1‑68 (MQ=255)

                      tGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGAcc                                       >  1:1262158/1‑68 (MQ=255)

                      tGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGAcc                                       >  1:1588148/1‑68 (MQ=255)

                      tGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGAcc                                       >  1:2589208/1‑68 (MQ=255)

                      tGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGAcc                                       >  1:2133806/1‑68 (MQ=255)

                      tGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGAcc                                       >  1:424830/1‑68 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:2926073/68‑1 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:1017626/68‑1 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:1226408/68‑1 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:922869/68‑1 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:229245/68‑1 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:251276/68‑1 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:2560357/68‑1 (MQ=255)

                         tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                    <  1:2672617/68‑1 (MQ=255)

                             gAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCt                                <  1:2469304/68‑1 (MQ=255)

                             gAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCt                                <  1:2614562/68‑1 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAg                                     >  1:2689006/1‑61 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCttg                              >  1:1566456/1‑66 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                              >  1:2234051/1‑68 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                              >  1:2184114/1‑68 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                              >  1:2165820/1‑68 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                              >  1:2145092/1‑68 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                              >  1:2575622/1‑68 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                              >  1:1237561/1‑68 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                              >  1:1416592/1‑68 (MQ=255)

                               aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTg                               >  1:294916/1‑67 (MQ=255)

                                 tCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGAtt                                                <  1:1838675/48‑1 (MQ=255)

                                         gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                   >  1:1946765/1‑69 (MQ=255)

                                         gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                   >  1:2098185/1‑69 (MQ=255)

                                         gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                   >  1:287552/1‑69 (MQ=255)

                                         gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                   >  1:3344517/1‑69 (MQ=255)

                                                          aaTCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGttt  <  1:1663532/69‑1 (MQ=255)

TGACGTGCGGAAGACATCAGTTTGCTCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTT  >  minE/2605048‑2605174

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