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 1,693,353 G→A 26.6% L289L (CTG→TTG)  iscS ← cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,693,3530GA26.6% 131.9 / 42.9 112L289L (CTG→TTG) iscScysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
Reads supporting (aligned to +/- strand):  ref base G (31/51);  new base A (17/13);  total (48/64)
Fisher's exact test for biased strand distribution p-value = 8.73e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 112 total aligned reads displayed.

TTCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGT  >  minE/1693291‑1693414
                                                              |                                                             
ttCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTaa                                                           >  1:3259728/1‑67 (MQ=255)
ttCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTaa                                                           >  1:422076/1‑67 (MQ=255)
ttCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTaa                                                           >  1:1942675/1‑67 (MQ=255)
ttCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAAc                                                         >  1:1013445/1‑69 (MQ=255)
ttCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAAc                                                         >  1:2555475/1‑69 (MQ=255)
ttCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAAc                                                         >  1:712822/1‑69 (MQ=255)
ttCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGGTCAGGTAAAc                                                         >  1:880744/1‑69 (MQ=255)
    aCGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAActtc                                                      <  1:3267151/68‑1 (MQ=255)
    aCGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAActtc                                                      <  1:2798290/68‑1 (MQ=255)
    aCGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAActtc                                                      <  1:1263460/68‑1 (MQ=255)
    aCGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAActtc                                                      <  1:1784149/68‑1 (MQ=255)
    aCGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAActtc                                                      <  1:1383835/68‑1 (MQ=255)
    aCGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGGCACCGTTCAGGTAAActtc                                                      <  1:2916645/68‑1 (MQ=255)
     cGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACTGTGTTCCAGGTCACCGTTCAGGTAAActtct                                                     >  1:2615313/1‑68 (MQ=255)
      gTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACttcttc                                                   <  1:3118178/69‑1 (MQ=255)
      gTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACttcttc                                                   <  1:106600/69‑1 (MQ=255)
        aGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACttcttc                                                   <  1:2835914/67‑1 (MQ=255)
         gTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGat                                                <  1:556519/69‑1 (MQ=255)
         gTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGat                                                <  1:3350421/69‑1 (MQ=255)
            gAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAActtc                                                      >  1:2326359/1‑60 (MQ=255)
            gAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             <  1:1521581/69‑1 (MQ=255)
            gAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             <  1:635643/69‑1 (MQ=255)
            gAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             <  1:307220/69‑1 (MQ=255)
            gAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:2094832/1‑69 (MQ=255)
            gAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:10982/1‑69 (MQ=255)
            gAAGCTGACGTTGAGAATGTTAGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAActtc                                                      >  1:147487/1‑60 (MQ=255)
             aaGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             <  1:821626/68‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:3411325/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:421853/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:318586/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:2945517/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:650842/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:732198/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:1012875/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:842803/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:2814174/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:1315766/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:1243260/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:2054228/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:2063159/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:2171007/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:1498487/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:1095598/69‑1 (MQ=255)
               gCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:1057266/69‑1 (MQ=255)
                cTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:3075772/68‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTATACTTCTTCGATATCTTTGATGcc                                    <  1:1381951/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:458048/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:2597221/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:915601/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:2995764/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:3179554/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:2477515/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:2119572/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:704275/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:896030/69‑1 (MQ=255)
                     gTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:2517664/69‑1 (MQ=255)
                       tGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGcc                                    <  1:394538/67‑1 (MQ=255)
                        gagaATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGt                                  >  1:3224759/1‑68 (MQ=255)
                        gagaATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGt                                  >  1:1777242/1‑68 (MQ=255)
                             tGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:166800/1‑52 (MQ=255)
                             tGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:2982652/1‑52 (MQ=255)
                             tGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:544385/1‑52 (MQ=255)
                             tGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:2631486/1‑52 (MQ=255)
                             tGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:2645372/1‑52 (MQ=255)
                             tGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATc                                             >  1:2678005/1‑52 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAgc                          >  1:1241940/1‑68 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:766495/1‑69 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:2288736/1‑69 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:1611576/1‑69 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:592853/1‑69 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:2684431/1‑69 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:2182492/1‑69 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:1655871/1‑69 (MQ=255)
                               ttCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGa                          >  1:2840956/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGTTGCCGATCCACAGACGGTTACGCAg               >  1:2941170/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:680175/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:83140/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:1212015/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:959945/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:1562965/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:3387542/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:1521722/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:3323282/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:3296672/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:2328066/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:22307/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:2190961/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:2124246/1‑69 (MQ=255)
                                          gtgtTCCAGGTCACCGTTCAAGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAg               >  1:1799562/1‑69 (MQ=255)
                                                cAGGTCACCGTTCAGGTAAACTTCTTCGATATCttt                                          <  1:950107/36‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:223578/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:2498517/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:2980795/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:755698/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:314713/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:3147292/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:3251426/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:3274579/68‑1 (MQ=255)
                                                        cGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:1618123/68‑1 (MQ=255)
                                                         gTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGt  <  1:606021/67‑1 (MQ=255)
                                                              |                                                             
TTCAACGTAGTTGAAGCTGACGTTGAGAATGTTCGGCGCACCGTGTTCCAGGTCACCGTTCAGGTAAACTTCTTCGATATCTTTGATGCCGTTCCACAGACGGTTACGCAGGCCGCGCAGACGT  >  minE/1693291‑1693414

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