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
A3 F50 I2 R1 257 49.9 1554294 99.0% 1538751 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,169,929 T→C R34R (CGT→CGC)  qseB → quorum sensing DNA‑binding response regulator in two‑component regulatory system with QseC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,169,9290TC98.0% 170.1 / ‑4.0 49R34R (CGT→CGC) qseBquorum sensing DNA‑binding response regulator in two‑component regulatory system with QseC
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (19/29);  total (19/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.65e-01

CGGTTTACTGGCAGCAAATACGGTTATCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGTCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGCGTGAGCCGGTACTGATCCTGACCGCGCGCGAT  >  NC_000913/3169786‑3170073
                                                                                                                                               |                                                                                                                                                
cGGTTTACTGGCAGCAAATACGGTTATCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGa                                                                                                                                            >  1:375069/1‑150 (MQ=255)
              caAATACGGTTATCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTtat                                                                                                                             <  1:772452/151‑1 (MQ=255)
                      gTTATCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCAcc                                                                                                                     >  2:310396/1‑151 (MQ=255)
                        tATCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCtt                                                                                                                   >  2:172702/1‑151 (MQ=255)
                        tATCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCt                                                                                                                    <  1:319032/150‑1 (MQ=255)
                         aTCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCtt                                                                                                                   <  2:236525/150‑1 (MQ=255)
                         aTCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCtt                                                                                                                   <  2:199544/150‑1 (MQ=255)
                           cGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTatg                                                                                                                >  2:328212/1‑151 (MQ=255)
                           cGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTat                                                                                                                 <  2:677840/150‑1 (MQ=255)
                              aGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGTCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTctgat                                                                                                              >  1:357601/1‑150 (MQ=255)
                              aGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTatgatg                                                                                                             <  2:206935/151‑1 (MQ=255)
                              aGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTatgatg                                                                                                             <  2:189226/151‑1 (MQ=255)
                                ggATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCg                                                                                                           <  1:564310/151‑1 (MQ=255)
                                  aTGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGt                                                                                                         >  2:173979/1‑151 (MQ=255)
                                   tGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTg                                                                                                        >  2:353548/1‑151 (MQ=255)
                                     aaaaaaTGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGAt                                                                                                      <  2:537616/151‑1 (MQ=255)
                                        aaaTGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCt                                                                                                   <  2:745022/151‑1 (MQ=255)
                                        aaaTGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCt                                                                                                   <  1:683288/151‑1 (MQ=255)
                                          aTGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTgg                                                                                                 >  1:300362/1‑151 (MQ=255)
                                            gCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGTCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGAt                                                                                               <  2:378754/151‑1 (MQ=255)
                                                aTTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTa                                                                                            >  1:365480/1‑150 (MQ=255)
                                                  tttACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAAc                                                                                          <  2:385010/150‑1 (MQ=255)
                                                    tACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCt                                                                                        <  1:272173/150‑1 (MQ=255)
                                                       tGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTAcc                                                                                    >  1:597771/1‑151 (MQ=255)
                                                           agaagaTGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGc                                                                                <  2:745452/151‑1 (MQ=255)
                                                             aagaTGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCat                                                                              <  1:767365/151‑1 (MQ=255)
                                                                aTGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCatgga                                                                           <  2:44429/151‑1 (MQ=255)
                                                                  gACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCatggat                                                                          <  2:475768/150‑1 (MQ=255)
                                                                     aTGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTc                                                                      <  2:430396/151‑1 (MQ=255)
                                                                         tGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTcgcg                                                                   >  1:15429/1‑150 (MQ=255)
                                                                             tGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGatat                                                               <  2:633180/150‑1 (MQ=255)
                                                                              ggCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATAtt                                                              <  2:742826/150‑1 (MQ=255)
                                                                                 gACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTg                                                           >  1:549813/1‑150 (MQ=255)
                                                                                  aCGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTgcg                                                         <  1:32964/151‑1 (MQ=255)
                                                                                   cGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTgcgc                                                        >  1:708244/1‑151 (MQ=255)
                                                                                             aCGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCgag                                              <  1:643669/151‑1 (MQ=255)
                                                                                               gggCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGaa                                            <  2:87950/151‑1 (MQ=255)
                                                                                                 gCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGaaa                                           >  2:545526/1‑150 (MQ=255)
                                                                                                     tAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAg                                        <  1:540421/149‑1 (MQ=255)
                                                                                                       gTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTc                                     >  2:625674/1‑150 (MQ=255)
                                                                                                       gTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTc                                     >  2:425402/1‑150 (MQ=255)
                                                                                                       gTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCa                                    <  2:212439/151‑1 (MQ=255)
                                                                                                         aaaaTGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGc                                  <  2:232247/151‑1 (MQ=255)
                                                                                                           aaTGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGCGt                                >  2:100978/1‑151 (MQ=255)
                                                                                                                gTTTTAGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCTCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATCTTTTTCGCGAATGGCGAGAAAAAGGTCAGCGTGAGcc                           <  1:574025/151‑1 (MQ=255)
                                                                                                                     aGCGTCGACTGGTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGCGTGAGCCGGTAc                      <  1:673073/151‑1 (MQ=255)
                                                                                                                               ggTTTACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGCGTGAGCCGGTACTGATCCTGAc            >  2:767210/1‑151 (MQ=255)
                                                                                                                                   tACACAAGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGCGTGAGCCGGTACTGATCCTGACcg          <  1:659337/149‑1 (MQ=255)
                                                                                                                                         aGGTCGCCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGCGTGAGCCGGTACTGATCCTGACCGCGCGCGAt  >  1:607290/1‑151 (MQ=255)
                                                                                                                                               |                                                                                                                                                
CGGTTTACTGGCAGCAAATACGGTTATCGCAGGGATGAAAAAATGCGAATTTTACTGATAGAAGATGACATGCTGATTGGCGACGGCATCAAAACGGGCCTTAGTAAAATGGGTTTTAGCGTCGACTGGTTTACACAAGGTCGTCAGGGAAAAGAGGCGCTTTATAGCGCACCTTATGATGCGGTGATCCTGGATTTAACCTTACCAGGCATGGATGGTCGCGATATTTTGCGCGAATGGCGAGAAAAAGGTCAGCGTGAGCCGGTACTGATCCTGACCGCGCGCGAT  >  NC_000913/3169786‑3170073

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A