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 1,882,543 T→C 35.8% E197E (GAA→GAG)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,882,5430TC35.8% 66.4 / 65.0 106E197E (GAA→GAG) relA(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand):  ref base T (40/28);  new base C (17/21);  total (57/49)
Fisher's exact test for biased strand distribution p-value = 2.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 106 total aligned reads displayed.

CAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTACACT  >  minE/1882480‑1882604
                                                               |                                                             
cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                                                          >  1:2261358/1‑69 (MQ=255)
cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                                                          >  1:1214323/1‑69 (MQ=255)
cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                                                          >  1:1940723/1‑69 (MQ=255)
cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                                                          >  1:1388132/1‑69 (MQ=255)
cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                                                          >  1:2380264/1‑69 (MQ=255)
cagcagTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCa                                                          >  1:3377752/1‑69 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:676439/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:41924/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:2043337/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:3425352/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:608927/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:3378177/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:1816819/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:1752842/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:1737417/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:3357433/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:814666/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:82555/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:3325428/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:3250587/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:2906138/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:1158111/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:2720051/69‑1 (MQ=255)
    agTTTTGCGATGCGTTTGTATTCGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTc                                                      <  1:932736/69‑1 (MQ=255)
          gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGt                                                >  1:2573965/1‑69 (MQ=255)
          gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGt                                                >  1:1259529/1‑69 (MQ=255)
          gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGt                                                >  1:2763577/1‑69 (MQ=255)
          gCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTACAGTTCCCATTTCAGTTg                                                 >  1:2082731/1‑68 (MQ=255)
                cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGAtt                                          >  1:630237/1‑69 (MQ=255)
                cGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGAt                                           >  1:1879769/1‑68 (MQ=255)
                   ttGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTcc                                        <  1:1009684/68‑1 (MQ=255)
                   ttGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTcc                                        <  1:902205/68‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:368475/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:2987386/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:2624758/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:866920/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:1288670/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:3304265/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:1329220/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:1646705/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:1938936/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:1942913/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:3418686/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:2197147/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:34957/54‑1 (MQ=255)
                    tGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:2014901/54‑1 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTgcc                                               >  1:1533228/1‑52 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACgg                                 >  1:2009878/1‑68 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:68216/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:3150077/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:3080652/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:902143/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:2765971/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:101507/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:1057763/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:13652/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:2081028/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:2250463/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:2384745/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:2391988/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:2497943/1‑69 (MQ=255)
                          cGGTCGGGTGCAGATAACGGAAGCAGTAATCTTCCAGCTCCCATTTCAGTTGCCCAATCCCAAGACGGt                                >  1:2582755/1‑69 (MQ=255)
                             ttGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTa                              <  1:2800472/68‑1 (MQ=255)
                                    gaGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCgg                      <  1:3414339/69‑1 (MQ=255)
                                     aGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCa                                                     <  1:1984371/37‑1 (MQ=255)
                                          aCGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTg                    >  1:2703474/1‑65 (MQ=255)
                                          aCGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTg                    >  1:751398/1‑65 (MQ=255)
                                          aCGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTg                    >  1:2955071/1‑65 (MQ=255)
                                          aCGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTg                    >  1:2985902/1‑65 (MQ=255)
                                          aCGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTa                <  1:388952/69‑1 (MQ=255)
                                          aCGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTa                <  1:3011918/69‑1 (MQ=255)
                                                   gTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGt       <  1:2997409/69‑1 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGtt                               >  1:2347577/1‑43 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTac     >  1:2976189/1‑69 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTac     >  1:2597128/1‑69 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTac     >  1:1124175/1‑69 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTac     >  1:344504/1‑69 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTac     >  1:2125650/1‑69 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTac     >  1:1264588/1‑69 (MQ=255)
                                                     aaTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTa      >  1:1699627/1‑68 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCTTAGa              >  1:1179977/1‑59 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGa              >  1:2380872/1‑59 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGa              >  1:89679/1‑59 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGa              >  1:1457291/1‑59 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGa              <  1:377140/59‑1 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTaca    >  1:3165560/1‑69 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTaca    >  1:2906250/1‑69 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTaca    >  1:2675768/1‑69 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTaca    >  1:1422265/1‑69 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTaca    >  1:909789/1‑69 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTaca    >  1:3305699/1‑69 (MQ=255)
                                                      aTCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTac     >  1:2497726/1‑68 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACgg                                 >  1:2094695/1‑38 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTacac   <  1:634684/68‑1 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTacac   <  1:1520306/68‑1 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTacac   <  1:2683391/68‑1 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTacac   <  1:879373/68‑1 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTACAct  >  1:548660/1‑69 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTACAct  >  1:403243/1‑69 (MQ=255)
                                                        cTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTACAct  >  1:2211859/1‑69 (MQ=255)
                                                               |                                                             
CAGCAGTTTGGCAATTCGTTTGTATTCGGTTGGATGGAGGTAACGGAAGCAGTAATCTTCCAGTTCCCATTTCAGTTGTCCGATTCCGAGACGGTTAGCCAGCGGTGCGTAGATGTTGGTACACT  >  minE/1882480‑1882604

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A