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
A10 F4 I0 R1 23 79.3 3792826 98.2% 3724555 99.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,535,612 A→C 100% I86S (ATC→AGC)  envZ ← sensory histidine kinase EnvZ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,535,6120AC100.0% 202.6 / ‑6.7 55I86S (ATC→AGC) envZsensory histidine kinase EnvZ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base C (28/26);  minor base G (1/0);  total (29/26)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGC  >  NC_000913/3535518‑3535707
                                                                                              |                                                                                               
gccCAGTTGCTGCGCCATTTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTGGTTGGAGTAGAGAGAGCTccc                                                                                             >  2:617449/1‑99 (MQ=255)
gccCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTccc                                                                                             <  2:438604/99‑1 (MQ=255)
 cccAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTcccc                                                                                            >  1:684948/1‑99 (MQ=255)
  ccAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCa                                                                                           <  2:1785694/99‑1 (MQ=255)
   cAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAg                                                                                          >  2:170147/1‑99 (MQ=255)
    aGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGc                                                                                         <  2:1500023/99‑1 (MQ=255)
           gcgcCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGt                                                                                  >  2:770301/1‑99 (MQ=255)
             gcCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAg                                                                                >  1:1627237/1‑99 (MQ=255)
                 tCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGAtct                                                                            <  1:885977/99‑1 (MQ=255)
                 tCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGAtct                                                                            <  2:1738068/99‑1 (MQ=255)
                 tCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGAtct                                                                            >  2:1354235/1‑99 (MQ=255)
                   tGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTcc                                                                          <  2:301934/99‑1 (MQ=255)
                    gATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTccc                                                                         <  2:468459/99‑1 (MQ=255)
                     aTGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGCGTAGAGAGAGGTCCCCAGCTCACGGTAGGTCTcccc                                                                        >  2:1739348/1‑98 (MQ=255)
                     aTGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCg                                                                        >  1:1749401/1‑99 (MQ=255)
                        gCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACg                                                                     >  1:1533890/1‑99 (MQ=255)
                          ttAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGa                                                                   >  2:71546/1‑99 (MQ=255)
                          ttAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGa                                                                   >  1:507306/1‑99 (MQ=255)
                           tAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGaa                                                                  <  2:1337086/99‑1 (MQ=255)
                           tAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGaa                                                                  >  1:976341/1‑99 (MQ=255)
                            aaGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCGGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGaaa                                                                 >  2:657378/1‑99 (MQ=255)
                                aTTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCgg                                                             >  2:558248/1‑99 (MQ=255)
                                  tCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGa                                                           >  1:321579/1‑99 (MQ=255)
                                     tAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGc                                                        >  1:777029/1‑99 (MQ=255)
                                     tAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGc                                                        >  2:742410/1‑99 (MQ=255)
                                     tAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGc                                                        >  2:231606/1‑99 (MQ=255)
                                        tgtTGCGCCCAAAGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGcaca                                                     >  2:809253/1‑99 (MQ=255)
                                          ttGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCAcaac                                                   <  1:845771/99‑1 (MQ=255)
                                              gcCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCAcaaccaac                                               <  1:1177347/99‑1 (MQ=255)
                                                ccAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTg                                             <  1:1438279/99‑1 (MQ=255)
                                                  aaCGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCg                                           <  1:1766582/99‑1 (MQ=255)
                                                   aCGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGt                                          >  2:1735365/1‑99 (MQ=255)
                                                   aCGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGt                                          <  1:589382/99‑1 (MQ=255)
                                                     gCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGc                                        <  2:1513975/99‑1 (MQ=255)
                                                      cAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGcc                                       <  2:534122/99‑1 (MQ=255)
                                                        gACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGt                                     >  2:1015834/1‑99 (MQ=255)
                                                        gACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGt                                     >  1:703369/1‑99 (MQ=255)
                                                           cTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGtcct                                  <  1:797409/99‑1 (MQ=255)
                                                           cTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGtcct                                  <  1:1891700/99‑1 (MQ=255)
                                                              ccTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCa                               >  2:1661831/1‑99 (MQ=255)
                                                                tctTCGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGt                             <  2:1766610/99‑1 (MQ=255)
                                                                    cGGCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCa                         >  2:263986/1‑99 (MQ=255)
                                                                     ggCAGCCTCGTTGGAGTAGGGGGAGCTCCCAAGCTCACGGTAGAGCTCCCGACGGAAAGCGGGAGGCCCAACCAACTGCGTGCCGTCTTCCAGTTGCAg                        <  2:66334/99‑1 (MQ=255)
                                                                     ggCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAg                        >  1:1610622/1‑99 (MQ=255)
                                                                     ggCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAg                        <  2:633435/99‑1 (MQ=255)
                                                                      gCAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGt                       >  1:156751/1‑99 (MQ=255)
                                                                       cAGCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGtt                      <  1:245108/99‑1 (MQ=255)
                                                                         gCCTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTg                    >  2:801931/1‑99 (MQ=255)
                                                                          ccTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGt                   <  2:1791652/99‑1 (MQ=255)
                                                                          ccTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGt                   <  2:1491116/99‑1 (MQ=255)
                                                                           cTCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAATTGCGTGCCGTCCTCCAGTTGCAGTTTGTc                  <  2:793211/99‑1 (MQ=255)
                                                                            tCGTTGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCg                 <  2:352402/99‑1 (MQ=255)
                                                                               ttGGAGTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGtc              >  1:586293/1‑99 (MQ=255)
                                                                                    gTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCaa         <  2:1622894/99‑1 (MQ=255)
                                                                                    gTAGAGAGAGCTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCaa         >  2:360649/1‑99 (MQ=255)
                                                                                       gagagagcTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACAt      >  2:1812255/1‑99 (MQ=255)
                                                                                        agagagcTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATa     <  1:59633/99‑1 (MQ=255)
                                                                                        agagagcTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATa     <  2:776089/99‑1 (MQ=255)
                                                                                        agagagcTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATa     <  2:1864495/99‑1 (MQ=255)
                                                                                         gagagcTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATAc    <  1:1213186/99‑1 (MQ=255)
                                                                                           gagcTCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGc  >  2:1700982/1‑99 (MQ=255)
                                                                                              |                                                                                               
GCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGC  >  NC_000913/3535518‑3535707

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A