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
A17 F172 I1 R1 29 81.4 1744314 96.7% 1686751 139.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 2,679,710 G→T G65V (GGC→GTC)  cbpD → possible secretory antigen

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,679,7100GT96.5% 179.3 / ‑0.8 57G65V (GGC→GTC) cbpDpossible secretory antigen
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base T (26/29);  total (27/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

CAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAC  >  CP000730/2679575‑2679846
                                                                                                                                       |                                                                                                                                        
cagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATg                                                                                                                                     >  1:570528/1‑141 (MQ=255)
 agATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGc                                                                                                                                    <  2:842417/141‑1 (MQ=255)
  gATTTCACTTATCAATCCGTCGAACAAACGCATCGATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCt                                                                                                                                   <  1:806880/141‑1 (MQ=255)
  gATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCt                                                                                                                                   <  1:552494/141‑1 (MQ=255)
   aTTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTa                                                                                                                                  <  1:326674/141‑1 (MQ=255)
      tCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTaaaa                                                                                                                               <  2:148078/141‑1 (MQ=255)
       cACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTaaaaa                                                                                                                              >  1:776530/1‑141 (MQ=255)
             tCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTa                                                                                                                        <  2:329747/141‑1 (MQ=255)
               aaTCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTAtt                                                                                                                      <  1:13708/141‑1 (MQ=255)
               aaTCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTAtt                                                                                                                      <  2:189231/141‑1 (MQ=255)
                 tCCGTCGAACAAACGCATCAATCGCATGCCTCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTAc                                                                                                                    >  2:328504/1‑141 (MQ=255)
                 tCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTAc                                                                                                                    <  2:281637/141‑1 (MQ=255)
                        aaCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCAc                                                                                                             >  1:819804/1‑141 (MQ=255)
                         aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACg                                                                                                            <  1:758863/141‑1 (MQ=255)
                             aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTaaa                                                                                                        >  1:723168/1‑141 (MQ=255)
                             aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTACTACAATGCACGTaaa                                                                                                        >  1:722839/1‑141 (MQ=255)
                               gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATc                                                                                                      <  1:721076/141‑1 (MQ=255)
                                cATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATTTACATGTTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCa                                                                                                     >  1:524815/1‑141 (MQ=255)
                                cATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCa                                                                                                     >  2:323267/1‑141 (MQ=255)
                                 aTCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCaa                                                                                                    <  2:147363/141‑1 (MQ=255)
                                    aaTCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAat                                                                                                 >  2:503706/1‑141 (MQ=255)
                                          aTGCCGCAGTTAATTATTATAGTAAAACCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGa                                                                                           <  2:198846/141‑1 (MQ=255)
                                          aTGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGa                                                                                           >  2:693042/1‑141 (MQ=255)
                                             ccGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTg                                                                                        >  2:226363/1‑141 (MQ=255)
                                                  gTTAATTATTATAGTAAACACCAATGTTCATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGt                                                                                   <  2:609602/141‑1 (MQ=255)
                                                       ttattaTAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAcc                                                                              <  2:18563/141‑1 (MQ=255)
                                                       ttattaTAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAcc                                                                              >  1:868747/1‑141 (MQ=255)
                                                              aGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGaaaa                                                                       >  2:145484/1‑141 (MQ=255)
                                                                tAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAAtt                                                                     <  1:223027/141‑1 (MQ=255)
                                                                   aaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGc                                                                  >  1:513654/1‑141 (MQ=255)
                                                                          tGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATg                                                           <  2:261640/141‑1 (MQ=255)
                                                                           gTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGc                                                          <  1:557679/141‑1 (MQ=255)
                                                                            tACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCa                                                         <  2:866740/141‑1 (MQ=255)
                                                                                  gtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAAc                                                   <  2:867759/141‑1 (MQ=255)
                                                                                     ggCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGc                                                <  2:776530/141‑1 (MQ=255)
                                                                                      gCATTTAAATGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCa                                               <  1:96338/141‑1 (MQ=255)
                                                                                       cATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGTGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAg                                              <  1:812029/141‑1 (MQ=255)
                                                                                       cATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAg                                              <  2:465091/141‑1 (MQ=255)
                                                                                       cATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCGAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAg                                              <  2:380066/141‑1 (MQ=255)
                                                                                             aaCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGAtatt                                        >  1:743966/1‑141 (MQ=255)
                                                                                              aCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGAtatta                                       >  1:560641/1‑141 (MQ=255)
                                                                                                  cgcgCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGa                                   >  1:795777/1‑141 (MQ=255)
                                                                                                     gcACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACAt                                >  2:782790/1‑141 (MQ=255)
                                                                                                     gcACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACAt                                >  2:173205/1‑141 (MQ=255)
                                                                                                        caAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc                             <  1:226363/141‑1 (MQ=255)
                                                                                                         aaGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCg                            >  2:374720/1‑141 (MQ=255)
                                                                                                         aaGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAACGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCg                            >  1:652475/1‑141 (MQ=255)
                                                                                                           gTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCa                          >  2:374226/1‑141 (MQ=255)
                                                                                                                tAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgttgt                     >  1:606673/1‑141 (MQ=255)
                                                                                                                   aCCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGa                  >  1:620222/1‑141 (MQ=255)
                                                                                                                    ccTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTAGTACACCAAGaaaa                                                                       >  1:727174/1‑87 (MQ=255)
                                                                                                                    ccTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTAGTACACCAAGaaaa                                                                       <  2:727174/87‑1 (MQ=255)
                                                                                                                      tGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACa               <  2:509912/141‑1 (MQ=255)
                                                                                                                        ttacTAATAGATGGGTCAATGCTAAAAATAGGTATTCCAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACTAg             >  2:600858/4‑141 (MQ=255)
                                                                                                                           cTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGtat          <  1:238865/141‑1 (MQ=255)
                                                                                                                              aTAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGtatata       <  1:628571/141‑1 (MQ=255)
                                                                                                                                   tGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAc  >  2:262768/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                        
CAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAC  >  CP000730/2679575‑2679846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A