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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,474,138 (A)6→7 coding (15/594 nt) bdcR → transcriptional repressor for divergent bdcA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,474,1321.A100.0% 200.2 / NA 62T3T (ACT→ACA) bdcRtranscriptional repressor for divergent bdcA
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (30/32);  total (30/32)

ACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTT  >  NC_000913/4473997‑4474261
                                                                                                                                        |                                                                                                                                 
aCCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaa                                                                                                                                >  2:1333645/1‑139 (MQ=255)
           gACTGCCAACGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATGAGGACTCCTTGATGTATTATGTAACATGCATTACAAAACTGTTTTAAATTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaaaaacaatatc                                                                                                                     >  1:1564381/1‑131 (MQ=255)
            aCTGCCACCGATGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTcg                                                                                                                     <  2:1045192/139‑1 (MQ=255)
            aCTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTcg                                                                                                                     <  2:1190279/139‑1 (MQ=255)
                ccACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGtt                                                                                                                 >  2:956505/1‑139 (MQ=255)
                ccACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGtt                                                                                                                 >  2:1135524/1‑139 (MQ=255)
                  aCCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTcg                                                                                                                     <  2:1214284/133‑1 (MQ=255)
                  aCCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTcg                                                                                                                     >  1:1214284/1‑133 (MQ=255)
                                             aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGa                                                                                    >  1:1607973/1‑139 (MQ=255)
                                                  cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAgg                                                                               >  2:1613274/1‑139 (MQ=255)
                                                         aaGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAAtctc                                                                        <  1:1333645/139‑1 (MQ=255)
                                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                >  1:1603007/1‑139 (MQ=255)
                                                                      tttATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                             >  2:407264/1‑105 (MQ=255)
                                                                      tttATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                             <  1:407264/105‑1 (MQ=255)
                                                                           tatGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCtttt                                                      >  2:1444701/1‑139 (MQ=255)
                                                                           tatGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCtttt                                                      >  2:82728/1‑139 (MQ=255)
                                                                           tatGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCtttt                                                      >  1:673503/1‑139 (MQ=255)
                                                                               tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTg                                                                                     <  2:652329/104‑1 (MQ=255)
                                                                               tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTg                                                                                     >  1:652329/1‑104 (MQ=255)
                                                                               tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCAc                                                  >  2:964140/1‑139 (MQ=255)
                                                                                 aCATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      <  1:1134014/69‑1 (MQ=255)
                                                                                 aCATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      >  2:1134014/1‑69 (MQ=255)
                                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           <  2:149852/77‑1 (MQ=255)
                                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           >  1:149852/1‑77 (MQ=255)
                                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCT‑CTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaaa                                            >  1:308407/1‑139 (MQ=255)
                                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           <  1:343403/74‑1 (MQ=255)
                                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           >  2:343403/1‑74 (MQ=255)
                                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAgg                                          >  1:1055579/1‑139 (MQ=255)
                                                                                         tACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGtt                                        >  1:910524/1‑139 (MQ=255)
                                                                                           cAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTc                                      >  1:229216/1‑139 (MQ=255)
                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      >  1:931938/1‑56 (MQ=255)
                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      <  2:931938/56‑1 (MQ=255)
                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt                                   <  2:1055579/139‑1 (MQ=255)
                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt                                   <  2:731356/139‑1 (MQ=255)
                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt                                   <  1:964140/139‑1 (MQ=255)
                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt                                   <  2:1607973/139‑1 (MQ=255)
                                                                                               aCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATg                                  <  1:1444701/139‑1 (MQ=255)
                                                                                                cTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGc                                 >  1:894971/1‑139 (MQ=255)
                                                                                                 tGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                   <  1:291005/88‑1 (MQ=255)
                                                                                                 tGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                   >  2:291005/1‑88 (MQ=255)
                                                                                                 tGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGATCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACTAAAAAGTTTTCgtttct                                >  2:1239285/1‑134 (MQ=255)
                                                                                                  gTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCT‑CTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                              <  2:308407/139‑1 (MQ=255)
                                                                                                   ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                              >  1:1463790/1‑139 (MQ=255)
                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      <  1:240047/41‑1 (MQ=255)
                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      >  2:240047/1‑41 (MQ=255)
                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAATGTTGCt                    >  2:152275/1‑139 (MQ=255)
                                                                                                                  aaCAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCGGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt               <  2:1564381/139‑1 (MQ=255)
                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCttttt                                                     <  1:602594/96‑1 (MQ=255)
                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCttttt                                                     >  2:602594/1‑96 (MQ=255)
                                                                                                                        ttttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGa         <  1:1613274/139‑1 (MQ=255)
                                                                                                                         tttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAt        <  1:463734/139‑1 (MQ=255)
                                                                                                                         tttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAt        <  1:1015062/139‑1 (MQ=255)
                                                                                                                          ttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt               >  2:1508102/1‑131 (MQ=255)
                                                                                                                          ttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt               <  1:1508102/131‑1 (MQ=255)
                                                                                                                             tAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATc    <  2:1603007/139‑1 (MQ=255)
                                                                                                                             tAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATc    <  2:229216/139‑1 (MQ=255)
                                                                                                                              aaTGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCt   <  2:910524/139‑1 (MQ=255)
                                                                                                                              aaTGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAATGTTGCTGAAGTTACTGATTATCt   <  1:152275/139‑1 (MQ=255)
                                                                                                                               aTGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCtt  <  2:1463790/139‑1 (MQ=255)
                                                                                                                               aTGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCtt  <  1:956505/139‑1 (MQ=255)
                                                                                                                                 ggTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaa                                              >  1:1014807/1‑93 (MQ=255)
                                                                                                                                 ggTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaa                                              <  2:1014807/93‑1 (MQ=255)
                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt               <  2:445030/123‑1 (MQ=255)
                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGt               >  1:445030/1‑123 (MQ=255)
                                                                                                                                        |                                                                                                                                 
ACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTT  >  NC_000913/4473997‑4474261

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A