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
A11 F142 I1 R1 99 64.8 3148104 96.3% 3031624 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,568,688 C→A intergenic (‑169/‑310) mdtM ← / → yjiP multidrug efflux system protein/pseudogene, transposase_31 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,568,6880CA100.0% 256.6 / NA 71intergenic (‑169/‑310)mdtM/yjiPmultidrug efflux system protein/pseudogene, transposase_31 family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (39/32);  total (39/32)

GTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTCGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAGTGTAATTAA  >  NC_000913/4568595‑4568784
                                                                                             |                                                                                                
gTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCa                                                                                            <  2:809908/100‑1 (MQ=255)
  gagaAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGa                                                                                          >  1:791895/1‑100 (MQ=255)
  gagaAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGa                                                                                          >  1:109879/1‑100 (MQ=255)
   agaAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGaa                                                                                         <  2:946276/100‑1 (MQ=255)
     aaGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAAt                                                                                        <  2:1016956/99‑1 (MQ=255)
      aGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGt                                                                                      <  1:1477742/100‑1 (MQ=255)
        ggCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGtat                                                                                    <  2:37978/100‑1 (MQ=255)
         gCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGtata                                                                                   >  2:1116417/1‑100 (MQ=255)
          cAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATaa                                                                                  <  2:869506/100‑1 (MQ=255)
           aaCGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAAc                                                                                 <  2:548902/100‑1 (MQ=255)
               agaCTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGAtt                                                                             >  2:1190598/1‑100 (MQ=255)
                gaCTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTa                                                                            <  1:567553/100‑1 (MQ=255)
                    gCAAATGTACTGAATTTCATGTAATCAACGACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACCATTACaaa                                                                        >  1:1470920/1‑100 (MQ=255)
                    gCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACaaa                                                                        <  1:1486194/100‑1 (MQ=255)
                    gCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACaaa                                                                        >  1:123577/1‑100 (MQ=255)
                    gCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACaaa                                                                        >  2:653223/1‑100 (MQ=255)
                    gCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACaaa                                                                        >  1:565689/1‑100 (MQ=255)
                     cAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAAt                                                                       <  1:1429384/100‑1 (MQ=255)
                       aaTGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAg                                                                     >  1:1381776/1‑100 (MQ=255)
                            aCTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGtcatc                                                                <  2:20872/100‑1 (MQ=255)
                             cTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGtcatca                                                               >  2:947508/1‑100 (MQ=255)
                                  tttCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGcaca                                                          <  1:823092/100‑1 (MQ=255)
                                       tGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTaca                                                     >  2:91130/1‑100 (MQ=255)
                                         tAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACAcc                                                   >  2:131927/1‑100 (MQ=255)
                                         tAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACAcc                                                   >  2:901250/1‑100 (MQ=255)
                                         tAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACAcc                                                   >  1:99432/1‑100 (MQ=255)
                                         tAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACAcc                                                   <  1:514235/100‑1 (MQ=255)
                                           aTCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACctc                                                 >  2:703313/1‑100 (MQ=255)
                                              aaCCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTg                                              >  2:1570321/1‑100 (MQ=255)
                                              aaCCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTg                                              <  2:1381766/100‑1 (MQ=255)
                                                ccACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGaa                                            >  1:439176/1‑100 (MQ=255)
                                                ccACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGaa                                            >  1:292781/1‑100 (MQ=255)
                                                  acacTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAAtt                                          >  2:1050534/1‑100 (MQ=255)
                                                  acacTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAAtt                                          >  2:726812/1‑100 (MQ=255)
                                                      tGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATg                                      <  2:734103/100‑1 (MQ=255)
                                                      tGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATg                                      <  2:225457/100‑1 (MQ=255)
                                                      tGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATg                                      <  1:703316/100‑1 (MQ=255)
                                                       gCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATgg                                     >  1:438758/1‑100 (MQ=255)
                                                         cTGTGAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGt                                   <  2:1271928/100‑1 (MQ=255)
                                                          tgtgAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGtt                                  >  1:451730/1‑100 (MQ=255)
                                                          tgtgAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGtt                                  <  1:91130/100‑1 (MQ=255)
                                                            tgAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGc                                <  2:109879/100‑1 (MQ=255)
                                                            tgAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGc                                <  2:1124226/100‑1 (MQ=255)
                                                             gAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCa                               <  1:1190605/100‑1 (MQ=255)
                                                             gAACACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCa                               >  2:497179/1‑100 (MQ=255)
                                                              aaCACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCAt                              >  2:806322/1‑100 (MQ=255)
                                                              aaCACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCAt                              >  2:152361/1‑100 (MQ=255)
                                                              aaCACACAGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCAt                              <  1:933730/100‑1 (MQ=255)
                                                                cacacaGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGTGTTGCATAg                            >  2:247748/1‑100 (MQ=255)
                                                                cacacaGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAg                            <  2:1314086/100‑1 (MQ=255)
                                                                  cacaGACAGAGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGaa                          >  2:900585/1‑100 (MQ=255)
                                                                       acagaGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAatat                     <  1:653226/100‑1 (MQ=255)
                                                                       acagaGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAatat                     <  2:1188909/100‑1 (MQ=255)
                                                                        cagaGAAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAAtata                    >  2:413600/1‑100 (MQ=255)
                                                                          gagaAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATaca                  >  2:853324/1‑100 (MQ=255)
                                                                          gagaAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATaca                  >  2:117349/1‑100 (MQ=255)
                                                                          gagaAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATaca                  >  2:315495/1‑100 (MQ=255)
                                                                            gaAATACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACAcc                <  2:1039302/100‑1 (MQ=255)
                                                                              aaTACTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTAATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCtt              >  1:686980/1‑100 (MQ=255)
                                                                                 aCTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAg           <  1:947516/100‑1 (MQ=255)
                                                                                  cTTTCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAgt          <  2:791890/100‑1 (MQ=255)
                                                                                   tttCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAgtg         <  1:315497/100‑1 (MQ=255)
                                                                                    ttCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCGTCAGCACATTACACCTCTTGAATTGATAGGTTGCATAGAAAATATACACCTTAAgtgt        >  1:1492622/1‑100 (MQ=255)
                                                                                    ttCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAgtgt        >  2:241432/1‑100 (MQ=255)
                                                                                    ttCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAgtgt        <  1:580533/100‑1 (MQ=255)
                                                                                    ttCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAgtgt        >  1:383174/1‑100 (MQ=255)
                                                                                     tCTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAGTGTa       <  2:48825/100‑1 (MQ=255)
                                                                                      cTGACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAGTGTaa      >  2:1215040/1‑100 (MQ=255)
                                                                                        gACTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAGTGTAAtt    >  1:1151080/1‑100 (MQ=255)
                                                                                          cTTAGGGTCAGCATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAGTGTAATTaa  >  2:825849/1‑100 (MQ=255)
                                                                                          cTTAGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAGTGTAATTaa  >  2:1200107/1‑100 (MQ=255)
                                                                                             |                                                                                                
GTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCAACCACACTGCCTGTGAACACACAGACAGAGAAATACTTTCTGACTTCGGGTCAGAATGTATAACGATTACAAATAGTCATCAGCACATTACACCTCTTGAATTGATGGGTTGCATAGAAAATATACACCTTAAGTGTAATTAA  >  NC_000913/4568595‑4568784

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A