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
A11 F1 I1 R1 757 76.1 3598070 93.4% 3360597 108.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,608,367 T→C I484T (ATC→ACC)  hyfF → hydrogenase 4, membrane subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,608,3670TC98.5% 230.3 / NA 65I484T (ATC→ACC) hyfFhydrogenase 4, membrane subunit
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (31/33);  minor base G (1/0);  total (32/33)
Fisher's exact test for biased strand distribution p-value = 4.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGCTGCGCGGGTGTTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCATCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCA  >  NC_000913/2608232‑2608501
                                                                                                                                       |                                                                                                                                      
tGGCTGCGCGGGTGTTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAg                                                                                                                                     >  1:1730533/1‑139 (MQ=255)
   cTGCGCGGGTGTTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGAt                                                                                                                                  >  2:522794/1‑139 (MQ=255)
    tGCGCGGGTGTTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATc                                                                                                                                 >  1:441909/1‑139 (MQ=255)
        cgGGTGTTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTgg                                                                                                                             >  1:618552/1‑139 (MQ=255)
            tgtTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTggtgac                                                                                                                         <  2:1125320/139‑5 (MQ=255)
            tgtTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTggcggg                                                                                                                         <  1:33416/139‑1 (MQ=255)
             gtTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTggcgggc                                                                                                                        <  1:522794/139‑1 (MQ=255)
               tAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGgcgc                                                                                                                      <  2:1503596/139‑1 (MQ=255)
                 aTGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCtt                                                                                                                    <  2:1747262/139‑1 (MQ=255)
                 aTGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCtt                                                                                                                    <  1:1504847/139‑1 (MQ=255)
                  tGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTc                                                                                                                   <  2:618552/139‑1 (MQ=255)
                  tGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGCGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTc                                                                                                                   <  1:1132688/139‑1 (MQ=255)
                     cGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCAc                                                                                                                >  2:998945/1‑139 (MQ=255)
                        aaCCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACtat                                                                                                             >  2:1464696/1‑139 (MQ=255)
                           cgccgcAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGt                                                                                                          <  1:1640152/139‑1 (MQ=255)
                           cgccgcAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGt                                                                                                          <  2:1730533/139‑1 (MQ=255)
                              cgcAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGt                                                                                                          >  1:694801/1‑136 (MQ=255)
                              cgcAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGt                                                                                                          <  2:694801/136‑1 (MQ=255)
                              cgcAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCct                                                                                                       >  1:487224/1‑139 (MQ=255)
                                    ccGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAgg                                                                                                 <  2:441909/139‑1 (MQ=255)
                                      gTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGa                                                                                               <  1:106414/139‑1 (MQ=255)
                                       ttAACCGGGGTGATCTCGACTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTc                                                                                                                   >  2:933467/1‑118 (MQ=255)
                                       ttAACCGGGGTGATCTCGACTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTc                                                                                                                   <  1:933467/118‑1 (MQ=255)
                                             ggggTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTc                                                                                                                   >  1:1387600/1‑112 (MQ=255)
                                             ggggTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTc                                                                                                                   <  2:1387600/112‑1 (MQ=255)
                                               ggTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATc                                                                                      >  2:599755/1‑139 (MQ=255)
                                               ggTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATc                                                                                      >  1:1109636/1‑139 (MQ=255)
                                                gTGATCTCAGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATct                                                                                     <  1:1093110/139‑1 (MQ=255)
                                                  gATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATctgc                                                                                   <  1:1464696/139‑1 (MQ=255)
                                                    tctcGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTggcgggc                                                                                                                        <  2:807415/100‑1 (MQ=255)
                                                    tctcGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTggcgggc                                                                                                                        >  1:807415/1‑100 (MQ=255)
                                                             gTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTggcggg                                                                                                                         >  2:1555737/1‑90 (MQ=255)
                                                             gTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTggcggg                                                                                                                         <  1:1555737/90‑1 (MQ=255)
                                                              ttGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTa                                                                       >  2:619335/1‑139 (MQ=255)
                                                                                     tCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCt                                                >  1:61619/1‑139 (MQ=255)
                                                                                          tgGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCAGCAGGATCCTGGCGGGCGCTTCCACt                                                                                                               >  1:1036490/1‑71 (MQ=255)
                                                                                          tgGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACt                                                                                                               <  2:1036490/71‑1 (MQ=255)
                                                                                          tgGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAgg                                           <  1:998945/139‑1 (MQ=255)
                                                                                            gTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAgg                                                                                                 >  1:84612/1‑83 (MQ=255)
                                                                                            gTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAgg                                                                                                 <  2:84612/83‑1 (MQ=255)
                                                                                            gTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCa                                         >  1:764603/1‑139 (MQ=255)
                                                                                             tCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCAc                                        <  1:916057/139‑1 (MQ=255)
                                                                                               atgatgCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGgcgc                                                                                                                      >  2:1285664/1‑59 (MQ=255)
                                                                                               atgatgCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGgcgc                                                                                                                      <  1:1285664/59‑1 (MQ=255)
                                                                                                  atgCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAGCGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCAt                                   <  2:1713023/139‑1 (MQ=255)
                                                                                                  atgCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCAt                                   <  1:932284/139‑1 (MQ=255)
                                                                                                  atgCTGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCAt                                   <  2:61619/139‑1 (MQ=255)
                                                                                                      tGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTg                                                   <  1:566123/119‑1 (MQ=255)
                                                                                                      tGGCGATGGGAACGCATATTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTg                                                   >  2:566123/1‑119 (MQ=255)
                                                                                                                       atTCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTg              <  2:764603/139‑1 (MQ=255)
                                                                                                                         tCCACAACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGaa            <  1:1250528/139‑1 (MQ=255)
                                                                                                                             caACCTGTCACCAGGATCCTGGCGGGCGCTTCCACtat                                                                                                             >  2:1700964/1‑38 (MQ=255)
                                                                                                                             caACCTGTCACCAGGATCCTGGCGGGCGCTTCCACtat                                                                                                             <  1:1700964/38‑1 (MQ=255)
                                                                                                                             caACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACg                                                                         <  2:584315/74‑1 (MQ=255)
                                                                                                                             caACCTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACg                                                                         >  1:584315/1‑74 (MQ=255)
                                                                                                                                ccTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGAttttt                                                     <  2:1639732/91‑1 (MQ=255)
                                                                                                                                ccTGTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGAttttt                                                     >  1:1639732/1‑91 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  1:1186589/1‑139 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  2:412403/1‑139 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  2:1650338/1‑139 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  2:1338966/1‑139 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  2:83185/1‑139 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  1:256597/1‑139 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  2:966165/1‑139 (MQ=255)
                                                                                                                                   gTCACCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCa  >  1:436536/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                                      
TGGCTGCGCGGGTGTTAATGGCGAAACCGCCGCAGGCCGTTAACCGGGGTGATCTCGGCTGGTTGACCACCTCGCCAATGGTGATTCTGCTGGTCATGATGCTGGCGATGGGAACGCATATTCCACAACCTGTCATCAGGATCCTGGCGGGCGCTTCCACTATAGTCCTCTCAGGGACGCACGATCTGCCTGCACAACGTAGCACCTGGCATGATTTTTTGCCTTCAGGCACCGCATCTGTTTCGGAGAAACACAGTGAACGTTAATTCA  >  NC_000913/2608232‑2608501

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A