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
A1 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,809,581	G→A	55.7%	G52G (GGG→GGA)	mprA →	DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,809,581	0	G	A	55.7%	38.6 / 154.6	114	G52G (GGG→GGA)	mprA	DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (22/28); new base A (25/38); total (47/67)
Fisher's exact test for biased strand distribution p-value = 7.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 120 total aligned reads displayed.

CGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCT  >  W3110S.gb/2809516‑2809647

cGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                 >  1:2956785/1‑69 (MQ=255)

 gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                >  1:724885/1‑69 (MQ=255)

    tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                >  1:507282/1‑66 (MQ=255)

    tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                >  1:2416113/1‑66 (MQ=255)

        catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                            <  1:1747769/66‑1 (MQ=255)

        catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                         >  1:827011/1‑69 (MQ=255)

            cacatggaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                     >  1:479360/1‑69 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCTCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1324570/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:3045593/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:2139674/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:432299/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:2814194/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1870388/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:2160364/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1618887/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:2187713/1‑69 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1258829/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:578766/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:2412064/69‑1 (MQ=255)

              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1354956/69‑1 (MQ=255)

               atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                  <  1:1269320/69‑1 (MQ=255)

               atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                  <  1:2899501/69‑1 (MQ=255)

               atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                  <  1:1876097/69‑1 (MQ=255)

               atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTCttt                                                  <  1:902028/69‑1 (MQ=255)

                tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:2108271/67‑1 (MQ=255)

                tacaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                <  1:942215/52‑1 (MQ=255)

                 gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                >  1:3169869/1‑69 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                              >  1:1211005/1‑54 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:2324714/65‑1 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:2585352/65‑1 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:3476847/65‑1 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   >  1:2264500/1‑65 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   >  1:3503229/1‑65 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                               >  1:709623/1‑69 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTAATg                                               >  1:2256501/1‑69 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAAGAGACgttgtt                                                   >  1:2635325/1‑65 (MQ=255)

                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                               >  1:209548/1‑69 (MQ=255)

                     agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                            >  1:1348566/1‑69 (MQ=255)

                      gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                              >  1:1695018/1‑66 (MQ=255)

                      gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                >  1:662626/1‑48 (MQ=255)

                      gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:1596811/1‑61 (MQ=255)

                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                          <  1:3128429/69‑1 (MQ=255)

                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                          <  1:3283112/69‑1 (MQ=255)

                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                          <  1:1003272/69‑1 (MQ=255)

                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                          <  1:34303/69‑1 (MQ=255)

                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                          <  1:844627/68‑1 (MQ=255)

                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                          <  1:1030865/68‑1 (MQ=255)

                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:3118972/1‑59 (MQ=255)

                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:1172939/1‑59 (MQ=255)

                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:624301/1‑59 (MQ=255)

                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:1424439/1‑59 (MQ=255)

                          gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:1230279/69‑1 (MQ=255)

                          gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACTAGACGTTGTTTATGGCGTTGAt                                       <  1:2386579/69‑1 (MQ=255)

                          gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:3004150/69‑1 (MQ=255)

                          gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:560177/69‑1 (MQ=255)

                          gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:1087051/69‑1 (MQ=255)

                            tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                     >  1:1984138/1‑69 (MQ=255)

                             gctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                    <  1:1959326/69‑1 (MQ=255)

                              ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:1293275/1‑53 (MQ=255)

                               tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                         <  1:2848886/62‑1 (MQ=255)

                                ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                   <  1:206796/67‑1 (MQ=255)

                                ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                   <  1:2236669/67‑1 (MQ=255)

                                 gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTAc                                    >  1:1522776/1‑65 (MQ=255)

                                 gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                  >  1:667072/1‑67 (MQ=255)

                                   gaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                               <  1:3400254/68‑1 (MQ=255)

                                   gaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                               <  1:1052719/68‑1 (MQ=255)

                                      ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                            >  1:2960764/1‑68 (MQ=255)

                                      ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                           <  1:1548539/69‑1 (MQ=255)

                                      ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                            >  1:1087467/1‑68 (MQ=255)

                                      ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                            >  1:2214398/1‑68 (MQ=255)

                                      ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                            >  1:2517511/1‑68 (MQ=255)

                                        gCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:1168886/43‑1 (MQ=255)

                                        gCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:3602480/43‑1 (MQ=255)

                                           aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:3362321/40‑1 (MQ=255)

                                            tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                      >  1:839811/1‑68 (MQ=255)

                                             aaaaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1137898/38‑1 (MQ=255)

                                              aaaTGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                   <  1:1751756/37‑1 (MQ=255)

                                              aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                   >  1:3345620/1‑69 (MQ=255)

                                              aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                   >  1:2202179/1‑69 (MQ=255)

                                              aaaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:1933102/1‑37 (MQ=255)

                                              aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                 <  1:583182/39‑1 (MQ=255)

                                              aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:2253642/49‑1 (MQ=255)

                                                   cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac              >  1:1665054/1‑69 (MQ=255)

                                                   cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac              >  1:2512211/1‑69 (MQ=255)

                                                   cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac              <  1:3372999/69‑1 (MQ=255)

                                                     gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                       >  1:2212702/1‑42 (MQ=255)

                                                     gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                       >  1:1171905/1‑42 (MQ=255)

                                                     gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca             <  1:2658287/68‑1 (MQ=255)

                                                     gAAGGCTCAGGGAATTATCGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAATCACAg            <  1:241457/69‑1 (MQ=255)

                                                     gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca             <  1:3613572/68‑1 (MQ=255)

                                                     gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg            <  1:2798895/69‑1 (MQ=255)

                                                        ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt         <  1:1634866/69‑1 (MQ=255)

                                                           tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa      <  1:1403929/69‑1 (MQ=255)

                                                           tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa      >  1:2416544/1‑69 (MQ=255)

                                                           tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa      >  1:2818256/1‑69 (MQ=255)

                                                               gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                        >  1:3214047/1‑47 (MQ=255)

                                                               gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                        <  1:1737660/47‑1 (MQ=255)

                                                               gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                        <  1:2755336/47‑1 (MQ=255)

                                                               gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                        <  1:2309224/47‑1 (MQ=255)

                                                               gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCt  >  1:153815/1‑69 (MQ=255)

CGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCT  >  W3110S.gb/2809516‑2809647

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