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 F1 I1 R1 759 65.2 3386260 90.7% 3071337 101.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,658,893 G→A *176* (TAG→TAA)  gadE → gad regulon transcriptional activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,658,8930GA100.0% 217.2 / NA 68*176* (TAG→TAA) gadEgad regulon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/33);  total (35/33)

GTCGACGCTCAATATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCA  >  NC_000913/3658776‑3659017
                                                                                                                     |                                                                                                                            
gTCGACGCTCAATATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGaaa                                                                                                         >  1:1552318/1‑139 (MQ=255)
 tCGACGCTCAATATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAAt                                                                                                        >  1:405645/1‑139 (MQ=255)
     cGCTCAATATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAt                                                                                                    <  1:1414273/139‑1 (MQ=255)
      gCTCAATATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGGAATTGAtg                                                                                                   >  1:123443/1‑139 (MQ=255)
        tCAATATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtggc                                                                                                 >  1:301085/1‑139 (MQ=255)
          aaTATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtggctg                                                                                               <  2:123443/139‑1 (MQ=255)
                 cGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGTATGAc                                                                                        >  2:1332167/1‑139 (MQ=255)
                 cGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGAc                                                                                        <  2:301085/139‑1 (MQ=255)
                    aacaaacaTTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAg                                                                                     >  1:697679/1‑139 (MQ=255)
                           aTTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCa                                                                              <  2:1552318/139‑1 (MQ=255)
                               aataTTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTTAGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATg                                                                          <  2:405645/136‑1 (MQ=255)
                                   ttCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGa                                                                      <  2:697679/139‑1 (MQ=255)
                                     cAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAt                                                                                                    >  2:1504127/1‑107 (MQ=255)
                                     cAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAt                                                                                                    <  1:1504127/107‑1 (MQ=255)
                                             cAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATg                                                                                <  1:587356/119‑1 (MQ=255)
                                             cAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATg                                                                                >  2:587356/1‑119 (MQ=255)
                                                    aTGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCACGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTg                                                     <  2:883119/139‑1 (MQ=255)
                                                      gTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGAATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGAt                                                   <  1:1332167/139‑1 (MQ=255)
                                                          aaGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTAccc                                                           >  2:1025394/1‑127 (MQ=255)
                                                          aaGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTAccc                                                           <  1:1025394/127‑1 (MQ=255)
                                                            gCTGAAACTAGGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGAc                                                                                        <  2:197654/96‑1 (MQ=255)
                                                            gCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGAc                                                                                        >  1:197654/1‑96 (MQ=255)
                                                            gCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACg                                                                                       <  1:186267/97‑1 (MQ=255)
                                                            gCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACg                                                                                       >  2:186267/1‑97 (MQ=255)
                                                            gCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTaa                                             >  1:449612/1‑139 (MQ=255)
                                                               gAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtggctggc                                                                                             <  1:1122318/88‑1 (MQ=255)
                                                               gAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtggctggc                                                                                             >  2:1122318/1‑88 (MQ=255)
                                                                aaaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAg                                                                                                                  >  2:864985/1‑66 (MQ=255)
                                                                aaaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAg                                                                                                                  <  1:864985/66‑1 (MQ=255)
                                                                aaaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCa                                                                              <  1:1505194/102‑1 (MQ=255)
                                                                aaaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCa                                                                              >  2:1505194/1‑102 (MQ=255)
                                                                aaaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGAt                                                   >  2:1439801/1‑129 (MQ=255)
                                                                aaaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGAt                                                   <  1:1439801/129‑1 (MQ=255)
                                                                 aaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACg                                                                                       >  1:1492722/1‑92 (MQ=255)
                                                                 aaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACg                                                                                       <  2:1492722/92‑1 (MQ=255)
                                                                 aaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGgag                                        >  1:781498/1‑139 (MQ=255)
                                                                 aaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGgag                                        >  2:382585/1‑139 (MQ=255)
                                                                 aaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGgag                                        >  1:320612/1‑139 (MQ=255)
                                                                 aaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGga                                         >  1:851616/1‑138 (MQ=255)
                                                                 aaCTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGga                                         <  2:851616/138‑1 (MQ=255)
                                                                      aGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATg                                                                                          >  1:1110565/1‑84 (MQ=255)
                                                                      aGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATg                                                                                          <  2:1110565/84‑1 (MQ=255)
                                                                              gAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTg                                                                       >  1:223776/1‑95 (MQ=255)
                                                                              gAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTg                                                                       <  2:223776/95‑1 (MQ=255)
                                                                                   aCATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGa                                                                      >  2:741471/1‑91 (MQ=255)
                                                                                   aCATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGa                                                                      <  1:741471/91‑1 (MQ=255)
                                                                                    cATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCAt                                                                >  2:1479680/1‑96 (MQ=255)
                                                                                    cATCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCAt                                                                <  1:1479680/96‑1 (MQ=255)
                                                                                     aTCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGCCGAGAGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTc                    >  1:549531/1‑139 (MQ=255)
                                                                                     aTCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTAccc                                                           <  2:256003/100‑1 (MQ=255)
                                                                                     aTCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTAccc                                                           >  1:256003/1‑100 (MQ=255)
                                                                                      tCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACtt                         <  1:668525/133‑1 (MQ=255)
                                                                                      tCGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACtt                         >  2:668525/1‑133 (MQ=255)
                                                                                       cGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTg                                                     <  1:794133/104‑1 (MQ=255)
                                                                                       cGTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTg                                                     >  2:794133/1‑104 (MQ=255)
                                                                                        gTCACCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTcccc                 <  2:781498/139‑1 (MQ=255)
                                                                                           aCCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtggct                                                                                                <  2:798854/57‑1 (MQ=255)
                                                                                           aCCCTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtggct                                                                                                >  1:798854/1‑57 (MQ=255)
                                                                                              cTGGGTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTAt           <  2:320612/139‑1 (MQ=255)
                                                                                                 ggTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCg                                                        >  2:945444/1‑91 (MQ=255)
                                                                                                 ggTATCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCg                                                        <  1:945444/91‑1 (MQ=255)
                                                                                                     tCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGAt                                                                           >  1:44939/1‑68 (MQ=255)
                                                                                                     tCACATCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGAt                                                                           <  2:44939/68‑1 (MQ=255)
                                                                                                      cacaTCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtgg                                                                                                  >  1:135019/1‑44 (MQ=255)
                                                                                                      cacaTCTTATTTTTAATCAGGACATAAGCAACTGAAATTGAtgg                                                                                                  <  2:135019/44‑1 (MQ=255)
                                                                                                       acaTCTTATTTTTAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATcca  >  2:1625683/1‑139 (MQ=255)
                                                                                                               tttttAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTa                                              <  2:528726/87‑1 (MQ=255)
                                                                                                               tttttAATCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTa                                              >  1:528726/1‑87 (MQ=255)
                                                                                                                     |                                                                                                                            
GTCGACGCTCAATATTTCGCAACAAACATTAAAGATTCAGAAATTCAACATTATGTACAAGCTGAAACTAAGACGTATGAGCGACATCGTCACCCTGGGTATCACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCA  >  NC_000913/3658776‑3659017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A