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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,471,432 T→C D29G (GAT→GGT)  yfdK ← CPS‑53 (KpLE1) prophage, conserved protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,471,4320TC100.0% 250.9 / NA 69D29G (GAT→GGT) yfdKCPS‑53 (KpLE1) prophage, conserved protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (33/36);  total (33/36)

TCCTCATGTGTTGGTGGTGGAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCATCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTAAAAGAAATTAACACCCT  >  NC_000913/2471303‑2471553
                                                                                                                                 |                                                                                                                         
tCCTCATGTGTTGATGGTGGAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATg                                                                                                                  >  1:1128810/1‑139 (MQ=255)
    cATGTGTTGGTGGTGGAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGcc                                                                                                              <  1:706468/139‑1 (MQ=255)
     aTGTGTTGGTGGTGGAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCa                                                                                                             >  1:244130/1‑139 (MQ=255)
         gtTGGTGGTGGAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCtt                                                                                                         >  2:441390/1‑139 (MQ=255)
            ggtggtggAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCg                                                                                                      >  2:1667112/1‑139 (MQ=255)
              tggtggAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCgtg                                                                                                    <  1:1667112/139‑1 (MQ=255)
                gtggAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTa                                                                                                  >  2:422157/1‑139 (MQ=255)
                  ggAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAAt                                                                                                <  2:1068931/139‑1 (MQ=255)
                          aGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTc                                                                                        <  1:441390/139‑1 (MQ=255)
                                tGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCtt                                                                                                         >  2:1371489/1‑116 (MQ=255)
                                tGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCtt                                                                                                         <  1:1371489/116‑1 (MQ=255)
                                tGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTcc                                                                                  >  1:634906/1‑139 (MQ=255)
                                tGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTcc                                                                                  >  1:1451037/1‑139 (MQ=255)
                                tGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTcc                                                                                  >  2:1208596/1‑139 (MQ=255)
                                tGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTcc                                                                                  <  1:1054679/139‑1 (MQ=255)
                                 gCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGcc                                                                                                                     >  1:418405/1‑103 (MQ=255)
                                 gCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGcc                                                                                                                     <  2:418405/103‑1 (MQ=255)
                                 gCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCa                                                                                 >  1:711607/1‑139 (MQ=255)
                                  cAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCaa                                                                                <  2:244130/139‑1 (MQ=255)
                                  cAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCaa                                                                                <  1:422157/139‑1 (MQ=255)
                                  cAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCaa                                                                                <  2:1327973/139‑1 (MQ=255)
                                  cAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCaa                                                                                <  2:1403818/139‑1 (MQ=255)
                                  cAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCaa                                                                                <  1:1208596/139‑1 (MQ=255)
                                                         aTACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcg                                                         <  2:1451037/139‑1 (MQ=255)
                                                            cGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGaa                                                                       <  1:17460/122‑1 (MQ=255)
                                                            cGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGaa                                                                       >  2:17460/1‑122 (MQ=255)
                                                                        ttCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCAt                                                                                      >  1:1217242/1‑95 (MQ=255)
                                                                        ttCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCAt                                                                                      <  2:1217242/95‑1 (MQ=255)
                                                                         tCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCa                                                                                 >  2:1167273/1‑99 (MQ=255)
                                                                         tCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCa                                                                                 <  1:1167273/99‑1 (MQ=255)
                                                                               gTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGGCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCAtttt                                   <  2:888062/139‑1 (MQ=255)
                                                                                tAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAggg                                                                             >  1:541270/1‑96 (MQ=255)
                                                                                tAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAggg                                                                             <  2:541270/96‑1 (MQ=255)
                                                                                tAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGCAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCAttttt                                  <  1:1139478/139‑1 (MQ=255)
                                                                                         aaaCTCAATATACACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGTATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATa                         <  2:1128810/139‑1 (MQ=255)
                                                                                                 tataCACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcg                                                         >  1:1036234/1‑99 (MQ=255)
                                                                                                 tataCACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcg                                                         <  2:1036234/99‑1 (MQ=255)
                                                                                                  ataCACTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTaaaa                <  2:634906/139‑1 (MQ=255)
                                                                                                      acTTGCTCATGAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGa                                                                        <  2:1039630/79‑1 (MQ=255)
                                                                                                      acTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGa                                                                        >  1:1039630/1‑79 (MQ=255)
                                                                                                      acTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCa                                <  2:1430345/119‑1 (MQ=255)
                                                                                                      acTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCa                                >  1:1430345/1‑119 (MQ=255)
                                                                                                       cTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTaa                  >  2:1418117/1‑132 (MQ=255)
                                                                                                       cTTGCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTaa                  <  1:1418117/132‑1 (MQ=255)
                                                                                                          gCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCAt                                                                                      <  1:162061/61‑1 (MQ=255)
                                                                                                          gCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCAt                                                                                      >  2:162061/1‑61 (MQ=255)
                                                                                                          gCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcgc                                                        <  1:585942/91‑1 (MQ=255)
                                                                                                          gCTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcgc                                                        >  2:585942/1‑91 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCCTGAGCCAGCTTGCGTGTaa                                                                                                 >  1:964640/1‑49 (MQ=39)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCgtg                                                                                                    <  2:1226859/46‑1 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCgtg                                                                                                    >  1:1226859/1‑46 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTaa                                                                                                 <  2:964640/49‑1 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGaaa                                                                      >  2:156309/1‑76 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGaaa                                                                      <  1:156309/76‑1 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGaaa                                                                      <  2:365312/76‑1 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGaaa                                                                      >  1:365312/1‑76 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTAAAAGAAATTAac       >  2:1532112/1‑139 (MQ=255)
                                                                                                           cTCATCAACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTAAAAGAAATTAac       >  1:1595486/1‑139 (MQ=255)
                                                                                                             catcaACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAAt                                          >  2:1527611/1‑102 (MQ=255)
                                                                                                             catcaACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAAt                                          <  1:1527611/102‑1 (MQ=255)
                                                                                                             catcaACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATa                         >  2:1400887/1‑119 (MQ=255)
                                                                                                             catcaACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATa                         <  1:1400887/119‑1 (MQ=255)
                                                                                                                caACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTcc                                                                                  >  2:921876/1‑59 (MQ=255)
                                                                                                                caACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTcc                                                                                  <  1:921876/59‑1 (MQ=255)
                                                                                                                caACTTCAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTAAAAGAAATTAACACCCt  >  1:100653/1‑139 (MQ=255)
                                                                                                                      cAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcgc                                                        <  1:448846/79‑1 (MQ=255)
                                                                                                                      cAACAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcgc                                                        >  2:448846/1‑79 (MQ=255)
                                                                                                                        aCAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcg                                                         >  1:666641/1‑76 (MQ=255)
                                                                                                                        aCAGCATCACCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcg                                                         <  2:666641/76‑1 (MQ=255)
                                                                                                                            catcacCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcg                                                         >  1:799873/1‑72 (MQ=255)
                                                                                                                            catcacCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTcg                                                         <  2:799873/72‑1 (MQ=255)
                                                                                                                             atcaccTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCAt                                                                                      >  1:230840/1‑42 (MQ=255)
                                                                                                                             atcaccTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCAt                                                                                      <  2:230840/42‑1 (MQ=255)
                                                                                                                                 |                                                                                                                         
TCCTCATGTGTTGGTGGTGGAATTTCAGACCATGCAGGAAAACCATTTTCTCCAGCGATACGGATTTTTCCTTTCGGCGGTAATCCGGAAAACTCAATATACACTTGCTCATCAACTTCAACAGCATCATCTGGCCATGAGCCAGCTTGCGTGTAATCCTCTTTCATCTCCAAGGGATAGAAAGAGTTTGTAGTCGCGGAATATATGTAATTCATTTTTCACTCCATAAAGTTAAAAGAAATTAACACCCT  >  NC_000913/2471303‑2471553

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