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
A12 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,392,100 T→C intergenic (‑72/+358) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,392,1000TC100.0% 221.2 / NA 60intergenic (‑72/+358)tldD/yhdPputative peptidase/DUF3971‑AsmA2 domains protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (28/32);  total (28/32)

TTCGCCGCTAGCAATTGTTCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTATCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAG  >  NC_000913/3391988‑3392230
                                                                                                                |                                                                                                                                  
ttCGCCGCTAGCAATTGTTCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTg                                                                                                          <  2:77094/139‑1 (MQ=255)
ttCGCCGCTAGCAATTGTTCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTg                                                                                                          <  1:768542/139‑1 (MQ=255)
ttCGCCGCTAGCAATTGTTCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTg                                                                                                          >  2:753522/1‑139 (MQ=255)
ttCGCCGCTAGCAATTGTTCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTg                                                                                                          >  2:241965/1‑139 (MQ=255)
     cgcTAGCAATTGTTCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGc                                                                                                     <  1:753522/139‑1 (MQ=255)
                 ttCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTAccc                                                                                                                                  >  2:1320144/1‑98 (MQ=255)
                 ttCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTAccc                                                                                                                                  <  1:1320144/98‑1 (MQ=255)
                 ttCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGc                                                                                         <  1:241965/139‑1 (MQ=255)
                    aCTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGcaca                                                                                      >  1:1307046/1‑139 (MQ=255)
                      ttACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCg                                                                                                               <  1:1284524/112‑1 (MQ=255)
                      ttACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCg                                                                                                               >  2:1284524/1‑112 (MQ=255)
                       tACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCg                                                                                   <  2:101247/139‑1 (MQ=255)
                            ggTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCa                                                                              <  1:3285/139‑1 (MQ=255)
                                       aTCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCg                                                                                   <  1:584032/123‑1 (MQ=255)
                                       aTCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCg                                                                                   >  2:584032/1‑123 (MQ=255)
                                       aTCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACgg                                                                   >  2:1374314/1‑139 (MQ=255)
                                       aTCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAAACGCACAGCGTCGCATCAGGCAACgg                                                                   >  1:499544/1‑139 (MQ=255)
                                           tttttGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGt                                                               <  1:1351882/139‑1 (MQ=255)
                                                   aCTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGTCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATgcg                                                       <  1:899943/139‑1 (MQ=255)
                                                   aCTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGAt                                                                                                >  2:1099498/1‑98 (MQ=255)
                                                   aCTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGAt                                                                                                <  1:1099498/98‑1 (MQ=255)
                                                          agttaCTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTaaa                                                <  1:1374314/139‑1 (MQ=255)
                                                            ttaCTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACg                                              <  2:1307046/139‑1 (MQ=255)
                                                              aCTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATg                                                         >  2:1157368/1‑126 (MQ=255)
                                                              aCTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATg                                                         <  1:1157368/126‑1 (MQ=255)
                                                               cTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCt                                           >  2:1040777/1‑139 (MQ=255)
                                                                 gCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTa                                         >  2:1205538/1‑139 (MQ=255)
                                                                 gCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTa                                         >  2:1005028/1‑139 (MQ=255)
                                                                   aGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATc                                       <  1:1040777/139‑1 (MQ=255)
                                                                   aGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATc                                       <  1:1005028/139‑1 (MQ=255)
                                                                     tAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTaaa                                                >  2:1306401/1‑128 (MQ=255)
                                                                     tAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTaaa                                                <  1:1306401/128‑1 (MQ=255)
                                                                     tAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCg                                     <  2:499544/139‑1 (MQ=255)
                                                                     tAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCg                                     <  2:389155/139‑1 (MQ=255)
                                                                     tAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCg                                     >  1:361486/1‑139 (MQ=255)
                                                                       gagGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGAc                                   <  1:1205538/139‑1 (MQ=255)
                                                                          gATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTa                                <  2:223121/139‑1 (MQ=255)
                                                                             tttttACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGca                                                                                        <  2:685961/80‑1 (MQ=255)
                                                                             tttttACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGca                                                                                        >  1:685961/1‑80 (MQ=255)
                                                                             tttttACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACgg                             <  2:361486/139‑1 (MQ=255)
                                                                               tttACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACg                                                                                          >  2:326686/1‑76 (MQ=255)
                                                                               tttACGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACg                                                                                          <  1:326686/76‑1 (MQ=255)
                                                                                  aCGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACg                                              <  2:915488/117‑1 (MQ=255)
                                                                                  aCGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACg                                              >  1:915488/1‑117 (MQ=255)
                                                                                  aCGGCTGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCATCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATg                        >  2:912537/1‑139 (MQ=255)
                                                                                       tGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCAt                                                                             >  1:1401526/1‑81 (MQ=255)
                                                                                       tGCCGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCAt                                                                             <  2:1401526/81‑1 (MQ=255)
                                                                                         ccGGATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGtt                 >  1:794972/1‑139 (MQ=255)
                                                                                            gATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGt              <  2:794972/139‑1 (MQ=255)
                                                                                            gATGCGGCGTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGACTTATCCGACCTACGGTTATGTTCCGTTTGt              <  1:912537/139‑1 (MQ=255)
                                                                                                cggcgTGAACGCCCTACCCAGCCTACGGTTATGTTCCg                                                                                                               <  1:792799/38‑1 (MQ=255)
                                                                                                cggcgTGAACGCCCTACCCAGCCTACGGTTATGTTCCg                                                                                                               >  2:792799/1‑38 (MQ=255)
                                                                                                   cgTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGc                                             <  2:583701/101‑1 (MQ=255)
                                                                                                   cgTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGc                                             >  1:583701/1‑101 (MQ=255)
                                                                                                   cgTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTg       >  2:394603/1‑139 (MQ=255)
                                                                                                   cgTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTg       >  1:1198388/1‑139 (MQ=255)
                                                                                                    gTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCg                                                                                   >  2:69273/1‑62 (MQ=255)
                                                                                                    gTGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCg                                                                                   <  1:69273/62‑1 (MQ=255)
                                                                                                     tGAACGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGAt     >  1:236853/1‑139 (MQ=255)
                                                                                                       aaCGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATaa   >  2:534005/1‑139 (MQ=255)
                                                                                                       aaCGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTAAGTTCCGTTTGTAGGCCTGATaa   >  2:1012656/1‑139 (MQ=255)
                                                                                                        aCGCCCTACCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAg  <  1:534005/139‑1 (MQ=255)
                                                                                                                |                                                                                                                                  
TTCGCCGCTAGCAATTGTTCACTTACCAGGTTAAGACTCATCGTTTTTGCTACTCGTTAGTTACTGCAGTAGAGGATTTTTTACGGCTGCCGGATGCGGCGTGAACGCCCTATCCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAG  >  NC_000913/3391988‑3392230

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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