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 2,340,914 C→T 25.6% A112A (GCC→GCT)  glnA → glutamine synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,340,9140CT25.6% 122.8 / 36.2 101A112A (GCC→GCT) glnAglutamine synthetase
Reads supporting (aligned to +/- strand):  ref base C (38/37);  new base T (18/8);  total (56/45)
Fisher's exact test for biased strand distribution p-value = 1.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 108 total aligned reads displayed.

GACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTCC  >  minE/2340849‑2340981
                                                                 |                                                                   
gACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCTATTGCGAAGCGCGCTGa                                                                   <  1:318576/68‑1 (MQ=255)
gACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCTATTGCGAAGCGCGCTGa                                                                   <  1:3214313/68‑1 (MQ=255)
gACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCTATTGCGAAGCGCGCTGa                                                                   <  1:3251355/68‑1 (MQ=255)
gACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCTATTGCGAAGCGCGCTGa                                                                   <  1:3074613/68‑1 (MQ=255)
gACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCTATTGCGAAGCGCGCTGa                                                                   <  1:657891/68‑1 (MQ=255)
gACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCTATTGCGAAGCGCGCTGa                                                                   <  1:2981423/68‑1 (MQ=255)
gACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCTATTGCGAAGCGCGCTGa                                                                   <  1:2754746/68‑1 (MQ=255)
    tCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGAtt                                                              <  1:2920231/69‑1 (MQ=255)
    tCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGAtt                                                              <  1:1843035/69‑1 (MQ=255)
    tCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGAtt                                                              <  1:1596427/69‑1 (MQ=255)
    tCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGAtt                                                              <  1:1315912/69‑1 (MQ=255)
    tCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGAtt                                                              <  1:982246/69‑1 (MQ=255)
    tCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGAtt                                                              <  1:1150961/69‑1 (MQ=255)
      cTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTa                                                             >  1:978717/1‑68 (MQ=255)
      cTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTAc                                                            >  1:2960264/1‑69 (MQ=255)
      cTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTAc                                                            >  1:2293123/1‑69 (MQ=255)
      cTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTAc                                                            >  1:2625455/1‑69 (MQ=255)
      cTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTAc                                                            >  1:341092/1‑69 (MQ=255)
      cTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTAc                                                            >  1:591299/1‑69 (MQ=255)
      cTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTAc                                                            >  1:774248/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAATCGCGCCGAAGATTACCt                                                          >  1:1430590/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:406900/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:408274/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:657681/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:2541779/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:2539224/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:2798026/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:1330598/1‑69 (MQ=255)
        tGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:169610/1‑69 (MQ=255)
        agAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCt                                                          >  1:3110754/2‑69 (MQ=255)
               ggCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCTAAGCGCGCCGAAGATTACCTGCGTTcc                                                   >  1:3096909/1‑69 (MQ=255)
                    cccgCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:3122889/66‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGTGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:2572860/69‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:3106630/69‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:871577/69‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:2295629/69‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:2855693/69‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:2822651/69‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:3373445/69‑1 (MQ=255)
                    ccTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTgg                                              <  1:475994/69‑1 (MQ=255)
                     cTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGc                                             <  1:984693/69‑1 (MQ=255)
                     cTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGc                                             <  1:1965935/69‑1 (MQ=255)
                     cTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGc                                             <  1:431505/69‑1 (MQ=255)
                     cTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGc                                             <  1:2600892/69‑1 (MQ=255)
                     cTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGc                                             <  1:2279509/69‑1 (MQ=255)
                      tGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGc                                             <  1:1649012/68‑1 (MQ=255)
                           ggCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGGCGAAGATTACCTGCGTTCCACTGGCATTGcc                                       <  1:1897646/69‑1 (MQ=255)
                                  aCCGTGACCCGCGCTCCATTGCGAAGCGCGCCGaa                                                                  >  1:907317/1‑35 (MQ=255)
                                  aCCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCg                                >  1:1970355/1‑69 (MQ=255)
                                  aCCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCg                                >  1:184145/1‑69 (MQ=255)
                                  aCCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCg                                >  1:2043776/1‑69 (MQ=255)
                                  aCCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCg                                >  1:683501/1‑69 (MQ=255)
                                  aCCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCg                                <  1:3167388/69‑1 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCAt                                           >  1:492862/1‑56 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGt                               >  1:2739189/1‑68 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2125066/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:1723436/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:3218225/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:1573115/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:3229916/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:521415/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:488897/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:1599098/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2828399/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2614446/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2722643/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2861652/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2877725/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2911511/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCTATTGCGAAGCGCGCTGAAGATTACCTGCGTTCTACTGGCATTGCCGACACCGTa                              >  1:2999739/1‑69 (MQ=255)
                                    cGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGt                               <  1:939413/68‑1 (MQ=255)
                                    cGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGt                               <  1:382544/68‑1 (MQ=255)
                                     gTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTAc                             >  1:2242233/1‑69 (MQ=255)
                                     gTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTAc                             >  1:983561/1‑69 (MQ=255)
                                     gTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACAACGTAc                             >  1:236784/1‑69 (MQ=255)
                                        aCCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGcc                                       >  1:1227555/1‑56 (MQ=255)
                                        aCCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGcc                                       >  1:1245442/1‑56 (MQ=255)
                                        aCCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGcc                                       >  1:3099144/1‑56 (MQ=255)
                                                 ccATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAg                 >  1:2016981/1‑69 (MQ=255)
                                                 ccATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAg                 >  1:351061/1‑69 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGaa               <  1:488072/68‑1 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAc              <  1:2634746/69‑1 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAc              <  1:2424765/69‑1 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAc              <  1:1806330/69‑1 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAc              <  1:1863103/69‑1 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAc              <  1:2878696/69‑1 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAc              <  1:1028315/69‑1 (MQ=255)
                                                    ttGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAc              <  1:1725818/69‑1 (MQ=255)
                                                      gCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAcc             >  1:2292153/1‑68 (MQ=255)
                                                      gCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAcc             >  1:1201048/1‑68 (MQ=255)
                                                      gCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAcc             >  1:2135151/1‑68 (MQ=255)
                                                      gCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAcc             >  1:275129/1‑68 (MQ=255)
                                                      gCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAAca             >  1:2112991/1‑67 (MQ=255)
                                                                ccGAATATTACCTGCGTTCCACTGGCATTGCAGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTcc  <  1:2433009/69‑1 (MQ=255)
                                                                ccGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTcc  <  1:2628217/69‑1 (MQ=255)
                                                                ccGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTcc  <  1:1273072/69‑1 (MQ=255)
                                                                ccGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTcc  <  1:2063520/69‑1 (MQ=255)
                                                                ccGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTcc  <  1:3401128/69‑1 (MQ=255)
                                                                 cGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTcc  <  1:1707349/68‑1 (MQ=255)
                                                                 cGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTcc  <  1:290798/68‑1 (MQ=255)
                                                                 |                                                                   
GACATCCTTGAACCTGGCACCCTGCAAGGCTATGACCGTGACCCGCGCTCCATTGCGAAGCGCGCCGAAGATTACCTGCGTTCCACTGGCATTGCCGACACCGTACTGTTCGGGCCAGAACCTGAATTCTTCC  >  minE/2340849‑2340981

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