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 I1 R1 765 39.6 1867486 94.4% 1762906 108.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,536,496 T→C Q30R (CAG→CGG)  ompR ← response regulator in two‑component regulatory system with EnvZ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,536,4960TC100.0% 186.4 / NA 51Q30R (CAG→CGG) ompRresponse regulator in two‑component regulatory system with EnvZ
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/24);  total (27/24)

GTTGCTCTGACTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCTGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAATTTGTAA  >  NC_000913/3536360‑3536619
                                                                                                                                        |                                                                                                                           
gTTGCTCTGACTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCgg                                                                                                                           <  2:349461/139‑1 (MQ=255)
         aCTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGt                                                                                                                  >  1:344006/1‑139 (MQ=255)
          cTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGtt                                                                                                                 <  1:420321/139‑1 (MQ=255)
           tACGAAGACCTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTc                                                                                                                <  1:594888/139‑1 (MQ=255)
              gAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGt                                                                                                             >  2:725070/1‑139 (MQ=255)
                   cGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGAt                                                                                                        <  1:337344/139‑1 (MQ=255)
                       ggCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACg                                                                                                    >  1:20175/1‑139 (MQ=255)
                                       aTCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacgc                                                                                    >  1:358611/1‑139 (MQ=255)
                                         cTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAg                                                                                  >  1:780607/1‑139 (MQ=255)
                                              ccAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCa                                                                             <  2:780607/139‑1 (MQ=255)
                                               cAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            >  2:738652/1‑107 (MQ=255)
                                               cAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            <  1:738652/107‑1 (MQ=255)
                                               cAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCAt                                                                            >  1:652635/1‑139 (MQ=255)
                                                  gTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATgtc                                                                         >  2:241789/1‑139 (MQ=255)
                                                       aTTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCAt                                                                    >  2:493185/1‑139 (MQ=255)
                                                       aTTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCAt                                                                    <  2:652635/139‑1 (MQ=255)
                                                           aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTc                                                                                                                <  2:168440/91‑1 (MQ=255)
                                                           aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTc                                                                                                                >  1:168440/1‑91 (MQ=255)
                                                           aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            >  2:446494/1‑95 (MQ=255)
                                                           aaTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            <  1:446494/95‑1 (MQ=255)
                                                            aTCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGacc                                                               >  1:914452/1‑139 (MQ=255)
                                                                 gTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAg                                                          >  2:748616/1‑139 (MQ=255)
                                                                 gTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAg                                                          >  1:77448/1‑139 (MQ=255)
                                                                          gATGGAAAGATTCACGAGTCAGCAGGCGACCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATg                                                                           <  2:486841/113‑1 (MQ=255)
                                                                          gATGGAAAGATTCACGAGTCAGCAGGCGACCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATg                                                                           >  1:486841/1‑113 (MQ=255)
                                                                           aTGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAg                                                <  2:344006/139‑1 (MQ=255)
                                                                               aaaGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTtct                                            <  2:77448/139‑1 (MQ=255)
                                                                                aaGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTtctc                                           >  1:119108/1‑139 (MQ=255)
                                                                                    ttCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGc                                       <  2:358611/139‑1 (MQ=255)
                                                                                     tCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCgg                                                                                                              <  1:401756/67‑1 (MQ=255)
                                                                                     tCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCgg                                                                                                              >  2:401756/1‑67 (MQ=255)
                                                                                      cACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTa                                                 >  1:455903/1‑127 (MQ=255)
                                                                                      cACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTa                                                 <  2:455903/127‑1 (MQ=255)
                                                                                             cagcagGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              <  2:119108/139‑1 (MQ=255)
                                                                                             cagcagGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              <  1:241789/139‑1 (MQ=255)
                                                                                                        ccATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              <  2:449676/128‑1 (MQ=255)
                                                                                                        ccATCTGTTCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCAttgtttgt                              >  1:449676/1‑128 (MQ=255)
                                                                                                               ttCTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGcaa            <  1:725070/139‑1 (MQ=255)
                                                                                                                 cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            >  1:380118/1‑41 (MQ=255)
                                                                                                                 cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTg                                                                                                            <  2:380118/41‑1 (MQ=255)
                                                                                                                 cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     >  2:727714/1‑64 (MQ=255)
                                                                                                                 cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     <  1:727714/64‑1 (MQ=255)
                                                                                                                 cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAAt                                                       >  1:53938/1‑94 (MQ=255)
                                                                                                                 cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAAt                                                       <  2:53938/94‑1 (MQ=255)
                                                                                                                 cTGCATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGcaaca          >  2:487825/1‑139 (MQ=255)
                                                                                                                    cATTAGCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAAtt       >  2:494584/1‑139 (MQ=255)
                                                                                                                         gCGACGCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAATTTGTaa  >  2:724659/1‑139 (MQ=255)
                                                                                                                              gCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     >  2:3904/1‑51 (MQ=255)
                                                                                                                              gCTTCGAACCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGcgcacg                                                                                     <  1:3904/51‑1 (MQ=255)
                                                                                                                                    aaCCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCa                                      <  1:648724/92‑1 (MQ=255)
                                                                                                                                    aaCCCGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCa                                      >  2:648724/1‑92 (MQ=255)
                                                                                                                                        |                                                                                                                           
GTTGCTCTGACTACGAAGACGTCGGCAAATCGACAAGCCATCTTCACCAGGTAACATTAAATCCAGTACCATAAGATGGAAAGATTCACGAGTCAGCAGGCGATCCATCTGTTCTGCATTAGCGACGCTTCGAACCTGGAAGCCTTGTTCGGTGAGATAACGTTCCAGCAGCGCACGCAGGCGCATGTCGTCATCGACCACCAGAATCTTGTAGTTCTCTTGCATTGTTTGTACTCCCAAAGGTTCGCAACAATTTGTAA  >  NC_000913/3536360‑3536619

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A