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 1,771,423 C→T 34.9% R331R (CGC→CGT)  pheA → fused chorismate mutase P and prephenate dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,771,4230CT34.9% 77.4 / 58.1 103R331R (CGC→CGT) pheAfused chorismate mutase P and prephenate dehydratase
Reads supporting (aligned to +/- strand):  ref base C (50/17);  new base T (18/18);  total (68/35)
Fisher's exact test for biased strand distribution p-value = 1.64e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

Only 100 of 103 total aligned reads displayed.

GCGCTGGTTGAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAG  >  minE/1771358‑1771487
                                                                 |                                                                
tcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:2597724/66‑1 (MQ=255)
gctcTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:615981/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:411001/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:3071728/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:156580/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:3224115/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:1385454/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:1380822/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:3067664/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:1304919/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:1665530/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:1686193/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:2699757/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:2456826/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:842044/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:914720/66‑1 (MQ=255)
gcacTGGTTGAAGCGTTGCTGGTACTGCGCAATCACAGTCTGATTATGACCCGTCTGGAATCACGTCCg                                                               <  1:2298290/66‑1 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGa                                                              >  1:1525662/1‑61 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACgg                                                       >  1:848213/1‑68 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGt                                                      >  1:1013991/1‑69 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGt                                                      >  1:2812022/1‑69 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGt                                                      >  1:2448156/1‑69 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGt                                                      >  1:1607150/1‑69 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGt                                                      >  1:3412327/1‑69 (MQ=255)
         gAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGt                                                      >  1:762637/1‑69 (MQ=255)
             cGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATc                                                  >  1:153395/1‑69 (MQ=255)
             cGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATc                                                  >  1:3184782/1‑69 (MQ=255)
             cGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATc                                                  >  1:1677394/1‑69 (MQ=255)
             cGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATc                                                  <  1:505691/69‑1 (MQ=255)
             cGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATc                                                  <  1:717695/69‑1 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAagag                                       >  1:576969/1‑64 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:394118/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:3002635/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:39752/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:50201/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:2715972/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:2428270/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:915404/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:1239461/1‑65 (MQ=255)
                             cAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAgaga                                      >  1:1823304/1‑65 (MQ=255)
                              aaCCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTc                                 <  1:2934491/69‑1 (MQ=255)
                               aCCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTc                                 <  1:2933602/68‑1 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGAt                                     >  1:661114/3‑59 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATg                                    >  1:2386185/3‑60 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:1763984/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:3416111/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:1420177/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:3106920/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:155004/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:3018866/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:273413/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:2559102/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:2513979/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:2161984/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:2228089/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:2272467/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:2405714/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:238381/3‑69 (MQ=255)
                                    agtCTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCTg                           >  1:110837/3‑69 (MQ=255)
                                    agacTGATTATGACCCGTCTGGAATCACGTCCGATTCACGGTAATCCGTGGGAAGAGATGTTTTATCt                            >  1:1668047/4‑68 (MQ=255)
                                    aaTCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTg                           <  1:1120143/69‑1 (MQ=255)
                                        tGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGata                       >  1:109321/1‑69 (MQ=255)
                                        tGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGata                       >  1:1296199/1‑69 (MQ=255)
                                        tGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGata                       >  1:1291761/1‑69 (MQ=255)
                                        tGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGata                       >  1:2298148/1‑69 (MQ=255)
                                        tGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGat                        >  1:823606/1‑68 (MQ=255)
                                                  ccGTCTGGAATCACGCCCGATTCACTGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:2924995/68‑1 (MQ=255)
                                                  ccGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:427015/68‑1 (MQ=255)
                                                  ccGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:3078393/68‑1 (MQ=255)
                                                  ccGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:1229024/68‑1 (MQ=255)
                                                  ccGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:1911425/68‑1 (MQ=255)
                                                  ccGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:777589/68‑1 (MQ=255)
                                                       tGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTg        >  1:1277500/1‑69 (MQ=255)
                                                       tGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTg        >  1:2726920/1‑69 (MQ=255)
                                                       tGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTg        <  1:3380412/69‑1 (MQ=255)
                                                           aTCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:1066601/59‑1 (MQ=255)
                                                           aTCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGa       <  1:2691359/66‑1 (MQ=255)
                                                           aTCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGa       <  1:1171020/66‑1 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGaa      >  1:1071069/1‑65 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGa       >  1:178202/1‑64 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:373392/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:2029387/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:190119/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:530316/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:525499/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:2863463/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:1659417/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:1290935/1‑69 (MQ=255)
                                                             cACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:1310392/1‑69 (MQ=255)
                                                              ccGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATc           >  1:168399/2‑59 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCa              <  1:2091866/56‑1 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAAt     >  1:2004182/1‑65 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:540018/1‑68 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:656262/1‑68 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:1153363/1‑68 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:2678678/1‑68 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:784546/1‑68 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:1481813/1‑68 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAg  >  1:2053405/1‑68 (MQ=255)
                                                              aCGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGCCCAATCtt         >  1:3119892/1‑61 (MQ=255)
                                                                 |                                                                
GCGCTGGTTGAAGCGTTGCTGGTACTGCGCAACCACAATCTGATTATGACCCGTCTGGAATCACGCCCGATTCACGGTAATCCATGGGAAGAGATGTTCTATCTGGATATTCAGGCCAATCTTGAATCAG  >  minE/1771358‑1771487

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