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 94 59.5 3027142 91.9% 2781943 108.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,351,093 G→A G190G (GGC→GGT)  dcuS ← sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,351,0930GA100.0% 233.3 / NA 66G190G (GGC→GGT) dcuSsensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (38/28);  total (38/28)

CGACGCCTTCTTTGATAGACTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATGCCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAATA  >  NC_000913/4350957‑4351220
                                                                                                                                        |                                                                                                                               
cgacgCCTTCTTTGATAGACTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATAcc                                                                                                                               >  2:286446/1‑139 (MQ=255)
     ccTTCTTTGATAGACTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAaata                                                                                                                          >  2:43462/1‑139 (MQ=255)
            tGATAGACTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGa                                                                                                                   <  1:364457/139‑1 (MQ=255)
                 gACTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGa                                                                                                              <  1:741297/139‑1 (MQ=255)
                  aCTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGAt                                                                                                             >  2:139410/1‑139 (MQ=255)
                  aCTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGAt                                                                                                             >  1:1506867/1‑139 (MQ=255)
                  aCTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGAt                                                                                                             >  2:555869/1‑139 (MQ=255)
                  aCTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGAt                                                                                                             >  1:1137833/1‑139 (MQ=255)
                    tGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATaa                                                                                                           >  1:1381200/1‑139 (MQ=255)
                    tGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATaa                                                                                                           >  1:1505753/1‑139 (MQ=255)
                        aCATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCt                                                                                                       <  1:555869/139‑1 (MQ=255)
                             gCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGc                                                                                                  >  2:1260582/1‑139 (MQ=255)
                               cTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGa                                                                                                <  2:721006/139‑1 (MQ=255)
                               cTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGa                                                                                                <  2:1506867/139‑1 (MQ=255)
                               cTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGa                                                                                                <  1:286446/139‑1 (MQ=255)
                                   cGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGAc                                                                                               >  2:423695/1‑136 (MQ=255)
                                   cGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGAc                                                                                               <  1:423695/136‑1 (MQ=255)
                                                 cGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTgg                                                                              >  2:1171478/1‑139 (MQ=255)
                                                 cGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTgg                                                                              >  1:519012/1‑139 (MQ=255)
                                                  gTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGAt                                                                                     <  1:1065199/131‑1 (MQ=255)
                                                  gTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGCACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGAt                                                                                     >  2:1065199/1‑131 (MQ=255)
                                                      agaTTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCGGATAATGCTCCAGCGAc                                                                                               <  1:943353/117‑1 (MQ=255)
                                                      agaTTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGAc                                                                                               >  2:943353/1‑117 (MQ=255)
                                                           tCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGa                                                                                                                   >  1:1462948/1‑92 (MQ=255)
                                                           tCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGa                                                                                                                   <  2:1462948/92‑1 (MQ=255)
                                                            cGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCt                                                                   <  2:1377375/139‑1 (MQ=255)
                                                                   ttCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCa                                                            >  1:1371476/1‑139 (MQ=255)
                                                                    tCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGa                                                                                                                   <  1:82962/83‑1 (MQ=255)
                                                                    tCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGa                                                                                                                   >  2:82962/1‑83 (MQ=255)
                                                                             aaaaGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAgg                                                         >  2:98130/1‑132 (MQ=255)
                                                                             aaaaGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAgg                                                         <  1:98130/132‑1 (MQ=255)
                                                                             aaaaGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCg                                                  >  1:322115/1‑139 (MQ=255)
                                                                                          tCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAAt                                     <  1:1260582/139‑1 (MQ=255)
                                                                                                   tAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGa                                                                                                              <  1:115668/57‑1 (MQ=255)
                                                                                                   tAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGa                                                                                                              >  2:115668/1‑57 (MQ=255)
                                                                                                   tAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTc                                                             <  1:1176758/106‑1 (MQ=255)
                                                                                                   tAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTc                                                             >  2:1176758/1‑106 (MQ=255)
                                                                                                     aCCAGAATGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGAt                          >  1:750556/1‑139 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAaataat                                                                                                                        <  1:855289/40‑1 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAaataat                                                                                                                        >  2:855289/1‑40 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGAc                                                                                                                  <  2:138669/46‑1 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGAc                                                                                                                  >  1:138669/1‑46 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGa                                                                                                <  2:675548/64‑1 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGa                                                                                                >  1:675548/1‑64 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCt                                                                   <  1:1295782/93‑1 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCt                                                                   >  2:1295782/1‑93 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCTCCACGCCAATTTGTTTATGATTTTCa                     >  1:122912/1‑139 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCa                     >  1:509066/1‑139 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCa                     >  1:1158952/1‑139 (MQ=255)
                                                                                                          aaTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCa                     >  2:583774/1‑139 (MQ=255)
                                                                                                           aTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAAc                                                               >  2:616335/1‑96 (MQ=255)
                                                                                                           aTGCAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAAc                                                               <  1:616335/96‑1 (MQ=255)
                                                                                                              cAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAAt                                     <  2:1026819/119‑1 (MQ=255)
                                                                                                              cAGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAAt                                     >  1:1026819/1‑119 (MQ=255)
                                                                                                               aGGTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTa                >  1:1398514/1‑139 (MQ=255)
                                                                                                                 gTGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGa              >  1:726569/1‑139 (MQ=255)
                                                                                                                  tGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGAt             <  2:726569/139‑1 (MQ=255)
                                                                                                                  tGCCAATCAGTCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGAt             <  1:583774/139‑1 (MQ=255)
                                                                                                                            tCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAAt   >  2:591691/1‑139 (MQ=255)
                                                                                                                            tCCGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAAt   >  1:826771/1‑139 (MQ=255)
                                                                                                                             ccGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCTCCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAATa  <  2:122912/139‑1 (MQ=255)
                                                                                                                             ccGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAATa  <  1:139410/139‑1 (MQ=255)
                                                                                                                             ccGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAATa  <  2:1505753/139‑1 (MQ=255)
                                                                                                                             ccGACCAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAATa  >  1:1397099/1‑139 (MQ=255)
                                                                                                                                 ccAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTg                                                                                       <  1:73831/50‑1 (MQ=255)
                                                                                                                                 ccAGCATACCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTg                                                                                       >  2:73831/1‑50 (MQ=255)
                                                                                                                                        |                                                                                                                               
CGACGCCTTCTTTGATAGACTGCAACATGGCCTGGCGTTGCTCAAACAGCGTGGAGATTTCGTAGGGTTCCAGGCCGAAAAGGATTTTTTTCAGTACCTTAACCAGAATGCAGGTGCCAATCAGTCCGACCAGCATGCCAAATAATACCGACCAGATAATGCTCCAGCGACTGTCATTGATCTGTTGGGTCACACGGCTTAACTCAAGGCCGATCGCCACCACGCCAATTTGTTTATGATTTTCATCGTAGATGGGGGTAAATA  >  NC_000913/4350957‑4351220

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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