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
A3 F1 I2 R1 777 59.2 2955938 92.5% 2734242 106.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,298,035 T→C E35G (GAA→GGA)  yraQ ← putative inner membrane permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,298,0350TC100.0% 206.8 / NA 60E35G (GAA→GGA) yraQputative inner membrane permease
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (31/29);  total (31/29)

CTTTCCATACCGCGAGGAAATAGATCATCGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTTCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAATAAGTTA  >  NC_000913/3297901‑3298160
                                                                                                                                      |                                                                                                                             
cTTTCCATACCGCGAGGAAATAGATCATCGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATTCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCa                                                                                                                           <  1:944116/139‑1 (MQ=255)
  ttCCATACCGCGAGGAAATAGATCATCGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCAtt                                                                                                                         <  1:147068/139‑1 (MQ=255)
      aTACCGCGAGGAAATAGATCATCGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTcac                                                                                                                     <  2:223706/139‑1 (MQ=255)
            cgAGGAAATAGATCATCGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCa                                                                                                               >  1:756139/1‑139 (MQ=255)
                          atcGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGa                                                                                                 >  2:1295082/1‑139 (MQ=255)
                           tcGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCa                                                                                                                           >  2:1145265/1‑112 (MQ=255)
                           tcGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCa                                                                                                                           <  1:1145265/112‑1 (MQ=255)
                             gcgTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACaa                                                                                              <  1:26839/139‑1 (MQ=255)
                               gTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACaa                                                                                              <  1:202287/137‑1 (MQ=255)
                               gTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACaa                                                                                              >  2:202287/1‑137 (MQ=255)
                                           cgccTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAgaga                                                                                                           >  2:266095/1‑112 (MQ=255)
                                           cgccTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAgaga                                                                                                           <  1:266095/112‑1 (MQ=255)
                                           cgccTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCATAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAgc                                                                                >  1:398629/1‑139 (MQ=255)
                                             ccTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATGCCAGAGACCGGCAATGACAACGAGAAAGAAAAgcgc                                                                              >  2:921518/1‑139 (MQ=255)
                                             ccTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAgcgc                                                                              >  1:509398/1‑139 (MQ=255)
                                             ccTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTAGCCGTAGTAAGGTCCCCGTTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAgcgc                                                                              >  1:945836/1‑139 (MQ=255)
                                                 ccATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGt                                                                          <  2:1422323/139‑1 (MQ=255)
                                                 ccATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCATAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGt                                                                          <  2:398629/139‑1 (MQ=255)
                                                  cATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTcccc                                                                                                                            <  2:1055205/88‑1 (MQ=255)
                                                  cATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTcccc                                                                                                                            >  1:1055205/1‑88 (MQ=255)
                                                           gCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCgg                                                                            >  2:353402/1‑127 (MQ=255)
                                                           gCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCgg                                                                            <  1:353402/127‑1 (MQ=255)
                                                                cGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACg                                                                                            <  1:1231312/106‑1 (MQ=255)
                                                                agCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACg                                                                                            >  2:1231312/2‑106 (MQ=255)
                                                                      cgcAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTccacca                                                                  >  2:219325/1‑126 (MQ=255)
                                                                      cgcAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTccacca                                                                  <  1:219325/126‑1 (MQ=255)
                                                                                     aCCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCt                                              >  1:22756/1‑131 (MQ=255)
                                                                                     aCCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGaa                                      >  1:1230975/1‑139 (MQ=255)
                                                                                     aCCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCACATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCt                                              <  2:22756/131‑1 (MQ=255)
                                                                                      ccGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCt                                              >  2:915074/1‑130 (MQ=255)
                                                                                      ccGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCt                                              <  1:915074/130‑1 (MQ=255)
                                                                                      ccGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCt                                              >  2:851942/1‑130 (MQ=255)
                                                                                      ccGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAg                                     >  1:826084/1‑139 (MQ=255)
                                                                                      ccGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAg                                     >  1:1023883/1‑139 (MQ=255)
                                                                                      ccGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATAACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGTCGTTGCCGTCt                                              <  1:851942/130‑1 (MQ=255)
                                                                                       cGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTc                                                                                                                       <  2:441146/56‑1 (MQ=255)
                                                                                       cGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTc                                                                                                                       >  1:441146/1‑56 (MQ=255)
                                                                                            cTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAgcgc                                                                              >  1:1263640/1‑92 (MQ=255)
                                                                                            cTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAgcgc                                                                              <  2:1263640/92‑1 (MQ=255)
                                                                                            cTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGAc                               <  1:112849/139‑1 (MQ=255)
                                                                                            cTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGAc                               <  1:1295082/139‑1 (MQ=255)
                                                                                             tgtgGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGAcc                              >  2:766191/1‑139 (MQ=255)
                                                                                               tgGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTccac                                                                    <  1:274520/99‑1 (MQ=255)
                                                                                               tgGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTccac                                                                    >  2:274520/1‑99 (MQ=255)
                                                                                               tgGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTc                                                                       <  1:691143/96‑1 (MQ=255)
                                                                                               tgGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTc                                                                       >  2:691143/1‑96 (MQ=255)
                                                                                                    ttCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATa                       >  1:1296717/1‑139 (MQ=255)
                                                                                                      cGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCa                                                                                                               <  2:1363432/49‑1 (MQ=255)
                                                                                                      cGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCa                                                                                                               >  1:1363432/1‑49 (MQ=255)
                                                                                                              gTAAACGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCa             >  1:642207/1‑139 (MQ=255)
                                                                                                                   cGCTTTGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAAt        <  1:766191/139‑1 (MQ=255)
                                                                                                                      tttGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCCCCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAATAAg     >  2:1004852/1‑139 (MQ=255)
                                                                                                                      tttGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAg                      >  1:765207/1‑122 (MQ=255)
                                                                                                                      tttGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAg                      <  2:765207/122‑1 (MQ=255)
                                                                                                                       ttGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAATAAGt    <  2:1296717/139‑1 (MQ=255)
                                                                                                                        tGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGAc                               <  1:1049607/111‑1 (MQ=255)
                                                                                                                        tGCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGAc                               >  2:1049607/1‑111 (MQ=255)
                                                                                                                         gCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCa                                                                                                     <  2:464876/40‑1 (MQ=255)
                                                                                                                         gCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCa                                                                                                     >  1:464876/1‑40 (MQ=255)
                                                                                                                         gCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAATAAGt    >  2:740819/1‑137 (MQ=255)
                                                                                                                         gCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAATAAGt    <  1:740819/137‑1 (MQ=255)
                                                                                                                         gCCGTAGTAAGGTCCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAATAAGTTa  <  2:756139/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                             
CTTTCCATACCGCGAGGAAATAGATCATCGCGTAATCCAACGCCGCCTGCCATGGGTTAGCATCCGCCTGCGCAAGGATAGATTTACCGATACTGTGGGTTTCGGCAGCAGTAAACGCTTTGCCGTAGTAAGGTTCCCATTTCACATACCAGAGACCGGCAATGACAACGAGAAAGAAAAGCGCGGGTTTCCACCACTGAATGGGCGTTGCCGCCTGAGATGAAGACTGACCAGTCATAGCATTCCCCAGGAATAAGTTA  >  NC_000913/3297901‑3298160

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A