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 2,499,362 T→C 33.7% D70D (GAT→GAC)  ilvN → acetolactate synthase I, small subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,499,3620TC33.7% 177.4 / 129.9 222D70D (GAT→GAC) ilvNacetolactate synthase I, small subunit
Reads supporting (aligned to +/- strand):  ref base T (86/61);  new base C (58/17);  total (144/78)
Fisher's exact test for biased strand distribution p-value = 7.22e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.24e-01

Only 100 of 225 total aligned reads displayed.

CAAAAGCCATATCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAGATCGCGGT  >  minE/2499296‑2499430
                                                                  |                                                                    
       cATATCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGaa                                                             <  1:744977/69‑1 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAATCTGGAAGATg                                                         >  1:814637/1‑69 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATg                                                         >  1:2187987/1‑69 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATg                                                         >  1:2790313/1‑69 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATg                                                         >  1:2051159/1‑69 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATg                                                         >  1:2910693/1‑69 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATg                                                         >  1:3171597/1‑69 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATg                                                         >  1:1720936/1‑69 (MQ=255)
           tCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATg                                                         >  1:142460/1‑69 (MQ=255)
            cTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGaa                                                             <  1:2462521/64‑1 (MQ=255)
                cTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGat                                                             <  1:3294408/60‑2 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:835959/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:1006113/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:3025666/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:672159/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:2793565/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:3317454/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:3324263/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:2193082/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   <  1:1359355/69‑1 (MQ=255)
                 tACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGt                                                     <  1:492931/67‑1 (MQ=255)
                  aCTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTTGAAGATGTCGTGaa                                                  <  1:1741600/69‑1 (MQ=255)
                       tCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGc                                             >  1:1384922/1‑69 (MQ=255)
                       tCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGc                                             >  1:3396932/1‑69 (MQ=255)
                        cAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCa                                            <  1:2230615/69‑1 (MQ=255)
                        cAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCa                                            <  1:2064833/69‑1 (MQ=255)
                        cAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCa                                            <  1:1899250/69‑1 (MQ=255)
                        cAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCa                                            <  1:1222335/69‑1 (MQ=255)
                             ccgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:2356728/2‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGGTAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:2740957/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTTGAAGATATCGTGAAAGTGCAGCGTa                                       >  1:2927655/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGt                                        >  1:334877/1‑68 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGt                                        >  1:2811313/1‑68 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGt                                        >  1:2846169/1‑68 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGt                                        >  1:1174072/1‑68 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGt                                        >  1:597280/1‑68 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGt                                        >  1:1523995/1‑68 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:1147297/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:2503158/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:850075/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:1739281/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:1214075/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:1655002/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:1647875/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:236581/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:660391/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:3371889/1‑69 (MQ=255)
                             acgacCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTa                                       >  1:93534/1‑69 (MQ=255)
                                    gCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGt                                 >  1:3094529/1‑68 (MQ=255)
                                    gCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGt                                 >  1:2280330/1‑68 (MQ=255)
                                    gCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGt                                 >  1:2018884/1‑68 (MQ=255)
                                    gCGTCTGGAGCAGATGATAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGt                                 >  1:150394/1‑68 (MQ=255)
                                       tCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGtccga                             >  1:2312118/1‑69 (MQ=255)
                                       tCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGtccga                             >  1:632967/1‑69 (MQ=255)
                                             gCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCcgac                       <  1:1767899/69‑1 (MQ=255)
                                             gCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCcgac                       <  1:1854549/69‑1 (MQ=255)
                                             gCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCcgac                       <  1:1875404/69‑1 (MQ=255)
                                             gCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCcgac                       <  1:2199916/69‑1 (MQ=255)
                                               aGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCcgac                       <  1:1918051/67‑1 (MQ=255)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:2440383/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:3336750/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:1499919/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:3422250/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:425562/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:1319323/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:1988921/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:2624147/1‑38 (MQ=21)
                                                gatgatAAGCCAGATAGACAAGCTGGAAGATGTGGTGa                                                   >  1:1057773/1‑38 (MQ=21)
                                                   gatAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGt                  >  1:1210174/1‑68 (MQ=255)
                                                   gatAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGt                  >  1:899623/1‑68 (MQ=255)
                                                    atAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                <  1:1293086/69‑1 (MQ=255)
                                                    atAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                <  1:2962883/69‑1 (MQ=255)
                                                    atAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                <  1:3002548/69‑1 (MQ=255)
                                                    atAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                <  1:1165509/69‑1 (MQ=255)
                                                    atAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                <  1:1068410/69‑1 (MQ=255)
                                                    atAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                <  1:1538796/69‑1 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:499468/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:1260119/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:1673508/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:3270343/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:2265892/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:180932/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:304494/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:2116509/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:2662222/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:2704786/1‑68 (MQ=255)
                                                     tAAGCCAGATAGACAAGCTGGAAGATGTGGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGtt                 >  1:2399890/1‑67 (MQ=255)
                                                     tAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:103787/1‑68 (MQ=255)
                                                     tAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:1041903/1‑68 (MQ=255)
                                                     tAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGttt                >  1:724064/1‑68 (MQ=255)
                                                      aaGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTa               <  1:1221066/68‑1 (MQ=255)
                                                       aGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTa               <  1:2121378/67‑1 (MQ=255)
                                                          cAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:1841657/69‑1 (MQ=255)
                                                          cAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:255903/69‑1 (MQ=255)
                                                          cAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:2512908/69‑1 (MQ=255)
                                                          cAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:1338919/69‑1 (MQ=255)
                                                          cAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:140190/69‑1 (MQ=255)
                                                          cAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:2432022/69‑1 (MQ=255)
                                                          cAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:1642470/69‑1 (MQ=255)
                                                          cAAATCGATAAGCTCGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAg          <  1:709466/69‑1 (MQ=255)
                                                                  |                                                                    
CAAAAGCCATATCTGGCTACTGGTCAATGACGACCAGCGTCTGGAGCAGATGATAAGCCAAATCGATAAGCTGGAAGATGTCGTGAAAGTGCAGCGTAATCAGTCCGATCCGACGATGTTTAACAAGATCGCGGT  >  minE/2499296‑2499430

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