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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,295,565 T→C F154F (TTT→TTC)  nrfE → heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,295,5650TC94.4% 364.7 / 7.5 108F154F (TTT→TTC) nrfEheme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
Reads supporting (aligned to +/- strand):  ref base T (6/0);  new base C (49/53);  total (55/53)
Fisher's exact test for biased strand distribution p-value = 2.71e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

Only 100 of 108 total aligned reads displayed.

TTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAGT  >  W3110S.gb/4295503‑4295631
                                                              |                                                                  
tttCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAcc                                                            >  1:2409553/1‑71 (MQ=255)
tttCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAcc                                                            >  1:2506738/1‑71 (MQ=255)
tttCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAcc                                                            >  1:737350/1‑71 (MQ=255)
tttCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAcc                                                            >  1:1492440/1‑71 (MQ=255)
tttCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:742194/1‑70 (MQ=255)
tttCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:2733219/1‑70 (MQ=255)
tttCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATACTGCAACATCCCGGTCTTATCTTCCATCCAcc                                                            >  1:3027675/1‑71 (MQ=255)
         gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:1628164/1‑61 (MQ=255)
         gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:2856368/1‑61 (MQ=255)
         gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:173507/1‑61 (MQ=255)
         gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:1513832/1‑61 (MQ=255)
         gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:1062847/1‑61 (MQ=255)
         gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                             >  1:449101/1‑61 (MQ=255)
          cAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTAc                                                  <  1:3929380/71‑1 (MQ=255)
          cAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTAc                                                  <  1:4055055/71‑1 (MQ=255)
          cAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTAc                                                  <  1:1507694/71‑1 (MQ=255)
          cAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTAc                                                  <  1:1542279/71‑1 (MQ=255)
          cAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTAc                                                  <  1:2521812/71‑1 (MQ=255)
           aaTCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCTCTGCTTTAc                                                  <  1:1272658/70‑1 (MQ=255)
           aaTCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTAc                                                  <  1:3800437/70‑1 (MQ=255)
                   gCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTAt                                         <  1:287687/71‑1 (MQ=255)
                         aTCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   >  1:2310358/1‑71 (MQ=255)
                         aTCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   >  1:1137163/1‑71 (MQ=255)
                         aTCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   >  1:1276124/1‑71 (MQ=255)
                         aTCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   >  1:1965102/1‑71 (MQ=255)
                           ctcAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:3858386/1‑62 (MQ=255)
                           ctcAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:665066/1‑62 (MQ=255)
                           ctcAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:3588962/1‑62 (MQ=255)
                           ctcAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:3638789/1‑62 (MQ=255)
                           ctcAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:364430/1‑62 (MQ=255)
                           ctcAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:3698605/1‑62 (MQ=255)
                            tcAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGttt                                 >  1:1488518/1‑70 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGttt                                 <  1:3274984/68‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGttt                                 <  1:2112240/68‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGttt                                 <  1:550213/68‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:3381666/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:3573061/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:2903388/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:2640087/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:762827/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:2283698/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:1354226/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:134954/66‑1 (MQ=255)
                              aaTCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:2161921/66‑1 (MQ=255)
                                tCCGATGCTGCAACATCCCGGGCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:4120908/64‑1 (MQ=255)
                                    aTGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTg                                              <  1:1170483/49‑1 (MQ=255)
                                    aTGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTg                                              <  1:2856669/49‑1 (MQ=255)
                                    aTGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgc                        >  1:3478857/1‑71 (MQ=255)
                                    aTGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTCACCTTg                                              <  1:526927/49‑1 (MQ=39)
                                     tgctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATg                                        >  1:3020271/1‑54 (MQ=255)
                                     tgctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       >  1:3084975/1‑71 (MQ=255)
                                     tgctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       >  1:507385/1‑71 (MQ=255)
                                     tgctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       >  1:2008172/1‑71 (MQ=255)
                                     tgctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       >  1:512183/1‑71 (MQ=255)
                                     ggctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGc                                      >  1:3746323/2‑56 (MQ=39)
                                     caatgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       <  1:2848067/68‑1 (MQ=255)
                                     caatgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       <  1:3605368/68‑1 (MQ=255)
                                     caatgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       <  1:2251506/68‑1 (MQ=255)
                                     caatgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       <  1:2415934/68‑1 (MQ=255)
                                     caatgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       <  1:2563569/68‑1 (MQ=255)
                                      aatgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                       <  1:1797121/68‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:340379/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:186835/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:1407819/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:3232563/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:2514128/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:3143247/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:3525561/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:1346410/71‑1 (MQ=255)
                                           aaCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGc                 <  1:2626766/71‑1 (MQ=255)
                                            aCATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTg                                              <  1:3186910/41‑1 (MQ=255)
                                              aTCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCt                                                >  1:2789699/1‑37 (MQ=255)
                                              aTCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCt                                           >  1:2229123/1‑42 (MQ=255)
                                              aTCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:2403912/1‑43 (MQ=255)
                                              aTCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:1245783/1‑43 (MQ=255)
                                              aTCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTa                                          >  1:297861/1‑43 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:3831392/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:1496466/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:3767779/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:3387002/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:2150771/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:3084050/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:3106325/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg             >  1:3222666/1‑71 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTg              >  1:1082018/1‑70 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTg              >  1:1166077/1‑70 (MQ=255)
                                               tCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTg              >  1:1922015/1‑70 (MQ=255)
                                                 ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGgc            <  1:3875939/70‑1 (MQ=255)
                                                 ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGgc            <  1:4112956/70‑1 (MQ=255)
                                                 ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGgc            <  1:3070304/70‑1 (MQ=255)
                                                   tgTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCt         >  1:2184697/2‑71 (MQ=255)
                                                   ggTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGt                                   <  1:2450386/45‑1 (MQ=255)
                                                    gTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                            <  1:3505901/35‑1 (MQ=255)
                                                    gTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                            <  1:261664/35‑1 (MQ=255)
                                                    gTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                            <  1:225243/35‑1 (MQ=255)
                                                    gTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                            <  1:1754036/35‑1 (MQ=255)
                                                    gTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                            <  1:1582618/35‑1 (MQ=255)
                                                         aTCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg   >  1:1806649/1‑71 (MQ=255)
                                                          tCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg   >  1:1866203/1‑70 (MQ=255)
                                                          tCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAGt  >  1:1407017/1‑71 (MQ=255)
                                                              |                                                                  
TTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAGT  >  W3110S.gb/4295503‑4295631

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