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 F28 I1 R1 162 93.0 3098984 99.0% 3067994 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 884,345 (G)5→4 coding (673/1233 nt) mdfA → multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913884,3410G.92.9% 160.0 / 7.3 42coding (669/1233 nt)mdfAmultidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter
Reads supporting (aligned to +/- strand):  ref base G (3/0);  new base . (0/39);  total (3/39)
Fisher's exact test for biased strand distribution p-value = 8.71e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.43e-01

CGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGG  >  NC_000913/884206‑884469
                                                                                                                                       |                                                                                                                                
cGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCggggc                                                                                                                              >  1:800173/1‑139 (MQ=255)
  cATTGGCAGCAATCTCTTTTTCCGGTCTGCAACGGGCCATGCTTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCggggcgc                                                                                                                            <  1:1534831/140‑4 (MQ=255)
     tGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCgggggggggg                                                                                                                         >  2:520309/1‑135 (MQ=255)
     tGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGggggcgg                                                                                                                         >  1:916514/1‑138 (MQ=255)
     gggCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCGCTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGggcgctgg                                                                                                                        <  2:858382/139‑1 (MQ=255)
       gCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCggggggcggggg                                                                                                                       >  2:818079/1‑133 (MQ=255)
        cAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGggcgctggcgc                                                                                                                     <  1:594621/140‑1 (MQ=255)
          gCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGgcgctggcgctg                                                                                                                   <  2:50896/140‑1 (MQ=255)
            gATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTggg                                                                                                                 <  1:188129/140‑1 (MQ=255)
                      ttCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGt                                                                                                       <  1:124526/140‑1 (MQ=255)
                       tCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTc                                                                                                      <  2:579243/140‑1 (MQ=255)
                          gTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGc                                                                                                   <  2:962496/140‑1 (MQ=255)
                               cAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTg                                                                                              <  1:1142454/140‑1 (MQ=255)
                               cAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTg                                                                                              <  2:772061/140‑1 (MQ=255)
                               cAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTg                                                                                              <  1:457797/140‑1 (MQ=255)
                               cAACGAGCCAGGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTg                                                                                              <  2:13764/140‑1 (MQ=255)
                                  cGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTg                                                                                           <  1:330998/140‑1 (MQ=255)
                                       cATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTg                                                                                      <  1:1060236/140‑1 (MQ=255)
                                              gAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGcc                                                                               <  1:1224588/140‑1 (MQ=255)
                                              gAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGcc                                                                               <  2:800173/140‑1 (MQ=255)
                                              gAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGcc                                                                               <  2:540050/140‑1 (MQ=255)
                                                    gCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCg                                                                         <  1:818079/140‑1 (MQ=255)
                                                     ccACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGG‑GCTGGCGCCGGGGGTCGTTTGTCTGCCGTTGCTTGCGGGGGTCGCCCCGTCGc                                                                        >  1:596635/1‑140 (MQ=255)
                                                     ccACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGc                                                                        <  1:46448/140‑1 (MQ=255)
                                                     ccACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGc                                                                        <  2:18459/140‑1 (MQ=255)
                                                     ccACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGc                                                                        <  2:1207935/140‑1 (MQ=255)
                                                        cgcgTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGa                                                                     <  1:559558/140‑1 (MQ=255)
                                                         gcgTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGAt                                                                    <  2:536298/140‑1 (MQ=255)
                                                          cgTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGAtt                                                                   <  1:520309/140‑1 (MQ=255)
                                                           gTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTa                                                                  <  1:1229186/140‑1 (MQ=255)
                                                                       aaCTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCg                                                      <  1:576066/140‑1 (MQ=255)
                                                                           gTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGa                                                  <  2:232016/140‑1 (MQ=255)
                                                                            tCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAg                                                 <  1:210049/140‑1 (MQ=255)
                                                                             cACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGc                                                <  1:1341339/140‑1 (MQ=255)
                                                                                       ccTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGagcag                                      <  1:1249940/139‑1 (MQ=255)
                                                                                        cTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGagcagc                                     <  2:109070/140‑1 (MQ=255)
                                                                                         tCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCt                                    <  1:272035/140‑1 (MQ=255)
                                                                                           ggTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTAt                                  <  1:448824/140‑1 (MQ=255)
                                                                                                   cTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATgg                          <  1:69962/140‑1 (MQ=255)
                                                                                                           tGGTGCTGAAGAACGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTtgctgc                  <  2:888603/140‑1 (MQ=255)
                                                                                                                  gaagaaCGGCCGCTTTGTGGCGGGGG‑GGTGGGGCGGGGGGTTGTTTGTTTTCCGTTTTTGGCGGGGGGGGCCCCCCCGCCGCGTATCATCATTACCCGCCGGCCGGTGGGGCGGCATGAATATGGGTTGCTGCCAggggc           >  2:1510897/1‑136 (MQ=255)
                                                                                                                  gaagaaCGGCCGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGcc           <  2:313552/140‑1 (MQ=255)
                                                                                                                           ccGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCgg  <  1:1258227/140‑1 (MQ=255)
                                                                                                                           ccGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCgg  <  1:358996/140‑1 (MQ=255)
                                                                                                                           ccGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCgg  <  2:1315055/140‑1 (MQ=255)
                                                                                                                           ccGCTTTGTGGC‑GGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGACGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCgg  <  1:1510897/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                
CGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGG  >  NC_000913/884206‑884469

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A