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 1,576,219 T→C 61.5% L275L (TTA→TTG)  xapB ← xanthosine transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,576,2190TC61.5% 45.7 / 52.6 83L275L (TTA→TTG) xapBxanthosine transporter
Reads supporting (aligned to +/- strand):  ref base T (16/16);  new base C (37/14);  total (53/30)
Fisher's exact test for biased strand distribution p-value = 5.95e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCCAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGA  >  minE/1576155‑1576284
                                                                |                                                                 
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:2457768/69‑1 (MQ=255)
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:3425575/69‑1 (MQ=255)
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:1292676/69‑1 (MQ=255)
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:2436243/69‑1 (MQ=255)
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:2410078/69‑1 (MQ=255)
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:307447/69‑1 (MQ=255)
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:1417020/69‑1 (MQ=255)
agCCAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:1474478/69‑1 (MQ=255)
  ccAAAGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:1293577/67‑1 (MQ=255)
   cAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCGAATCGCTTTAAAAAGa                                                            >  1:1796625/1‑69 (MQ=255)
   cAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGa                                                            >  1:2745226/1‑69 (MQ=255)
   cAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGa                                                            >  1:299675/1‑69 (MQ=255)
   cAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGa                                                            >  1:1642719/1‑69 (MQ=255)
   cAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGa                                                            >  1:2576754/1‑69 (MQ=255)
   cAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGa                                                            >  1:1130899/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:2254404/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:807654/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:709589/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:2798880/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:2699936/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:1979483/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:1878450/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:793250/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:2530902/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:601121/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:483524/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:533103/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:585433/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:1313507/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:3177114/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:178617/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:3074580/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:1558652/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:1562002/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:83008/1‑69 (MQ=255)
    aaaGCGCAGCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGaa                                                           >  1:3014563/1‑69 (MQ=255)
            gCGTCCACGCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCaaaa                                                               <  1:164067/57‑1 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGtata                                           <  1:2361101/69‑1 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGtata                                           <  1:2884267/69‑1 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGtata                                           <  1:2690014/69‑1 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTAAGtata                                           <  1:441364/69‑1 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTAtc                                                    >  1:1036540/1‑59 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAg                                               >  1:697944/1‑65 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:2299568/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:1435194/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:3161728/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:1615956/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:2536945/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:1311485/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:602423/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:1182347/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:886772/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:532439/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:1143667/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:2556439/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:665773/1‑68 (MQ=255)
                    gCCACCATACTCATCAGCATGACGGTTTTAATACAGAAACGCTTCAAAAAGAACGGTATCGTCAGaat                                            >  1:1970310/1‑68 (MQ=255)
                                         aCGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCtg                       >  1:3429267/1‑68 (MQ=255)
                                             ttttAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaaa                  <  1:1784649/69‑1 (MQ=255)
                                             ttttAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaaa                  <  1:235661/69‑1 (MQ=255)
                                             ttttAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaaa                  <  1:2650624/69‑1 (MQ=255)
                                                     ccAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAg           >  1:2070951/1‑68 (MQ=255)
                                                     ccAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAg           >  1:2691599/1‑68 (MQ=255)
                                                        aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa       <  1:1472237/66‑1 (MQ=255)
                                                        aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa       <  1:1320875/66‑1 (MQ=255)
                                                        aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa       <  1:3231138/66‑1 (MQ=255)
                                                        aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa       <  1:2510358/66‑1 (MQ=255)
                                                           cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa      >  1:725445/1‑67 (MQ=255)
                                                           cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa      >  1:89249/1‑67 (MQ=255)
                                                           cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa      >  1:46413/1‑67 (MQ=255)
                                                           cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa      >  1:2524813/1‑67 (MQ=255)
                                                           cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaa       >  1:1144673/1‑66 (MQ=255)
                                                           cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaa       >  1:3302897/1‑66 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaa                   <  1:2995924/53‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg   <  1:396346/69‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg   <  1:1817558/69‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg   <  1:716408/69‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg   <  1:706163/69‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg   <  1:682569/69‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg   <  1:647722/69‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg   >  1:3105921/1‑69 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCAGTGAAACTGACAGTAAAATgg   <  1:1892274/69‑1 (MQ=255)
                                                            gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTCCTGCCATCTGTGAAACTGACAGTAAAATgg   <  1:172555/69‑1 (MQ=255)
                                                              tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTTAAACTGACAGTAAAATGGa  <  1:1755786/68‑1 (MQ=255)
                                                              tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa  <  1:2540205/68‑1 (MQ=255)
                                                              tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa  <  1:2131803/68‑1 (MQ=255)
                                                              tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa  <  1:387235/68‑1 (MQ=255)
                                                              tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa  <  1:1110894/68‑1 (MQ=255)
                                                                |                                                                 
AGCCAAAGCGCAGCGTCCAGGCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGA  >  minE/1576155‑1576284

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