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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,805,475 T→C N159S (AAT→AGT)  waaP ← kinase that phosphorylates core heptose of lipopolysaccharide

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,805,4750TC100.0% 265.2 / NA 74N159S (AAT→AGT) waaPkinase that phosphorylates core heptose of lipopolysaccharide
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (33/41);  total (33/41)

GCCCGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAATC  >  NC_000913/3805379‑3805569
                                                                                                |                                                                                              
gCCCGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCCGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTa                                                                                             >  1:551042/1‑100 (MQ=255)
gCCCGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTa                                                                                             >  1:710822/1‑100 (MQ=255)
  ncGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATc                                                                                           >  2:596351/2‑100 (MQ=255)
      tGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTg                                                                                       >  1:1080994/1‑100 (MQ=255)
        cAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCa                                                                                     >  2:869981/1‑100 (MQ=255)
        cAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCa                                                                                     <  1:367217/100‑1 (MQ=255)
        cAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCa                                                                                     >  1:860395/1‑100 (MQ=255)
         aGATCGATAACTGACATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAg                                                                                    <  1:310183/100‑1 (MQ=255)
         aGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAg                                                                                    <  1:590124/100‑1 (MQ=255)
         aGATCGATAACTGAAATTTTTAATTCATCTGCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAg                                                                                    <  1:218491/100‑1 (MQ=255)
          gATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGt                                                                                   <  2:710820/100‑1 (MQ=255)
           aTCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTa                                                                                  <  1:1464922/100‑1 (MQ=255)
           aTCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTa                                                                                  <  1:88816/100‑1 (MQ=255)
           aTCGATAACTGAAAATTTTAATTCATCTTCCCGGCAAGTAAATAAAAAAAAAAAAAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTa                                                                                  <  2:783936/100‑1 (MQ=255)
                     gAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTAc                                                                        >  2:1045775/1‑100 (MQ=255)
                      aaaTTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACg                                                                       <  1:1194652/100‑1 (MQ=255)
                       aaTTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCCAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGc                                                                      <  2:875172/100‑1 (MQ=255)
                       aaTTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGc                                                                      <  1:1108217/100‑1 (MQ=255)
                              aaTTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAg                                                               <  1:1315442/100‑1 (MQ=255)
                                  cATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGc                                                           <  1:619577/100‑1 (MQ=255)
                                   aTCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCt                                                          <  2:397372/100‑1 (MQ=255)
                                      ttCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATACATTTTACGCACCATAGTTGCTaca                                                       <  1:853807/100‑1 (MQ=255)
                                       tCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTacac                                                      >  1:1352433/1‑100 (MQ=255)
                                       tCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTacac                                                      >  2:330952/1‑100 (MQ=255)
                                        cccGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACg                                                     >  2:698216/1‑100 (MQ=255)
                                         ccGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGt                                                    >  1:1327502/1‑100 (MQ=255)
                                          cGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACgcg                                                   >  1:471416/1‑98 (MQ=255)
                                          cGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTg                                                   <  1:596353/100‑1 (MQ=255)
                                              cAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAAGAGTCGCGGTTACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGAt                                               <  1:243630/100‑1 (MQ=255)
                                               ttccgatctcAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATc                                              <  2:1403569/91‑1 (MQ=255)
                                               aGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATc                                              >  2:506649/1‑100 (MQ=255)
                                               aGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATc                                              <  1:570710/100‑1 (MQ=255)
                                                gTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCa                                             >  2:205797/1‑100 (MQ=255)
                                                 tAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGCCTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAg                                            >  1:664432/1‑100 (MQ=255)
                                                  aaaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGc                                           <  1:876333/100‑1 (MQ=255)
                                                  aaaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGc                                           >  1:862584/1‑100 (MQ=255)
                                                  aaaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGc                                           <  1:56917/100‑1 (MQ=255)
                                                  aaaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGc                                           >  2:392632/1‑100 (MQ=255)
                                                  aaaTGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGc                                           <  1:1287415/100‑1 (MQ=255)
                                                        cAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAgatcggaa                                     >  1:1403577/1‑93 (MQ=255)
                                                        cAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGc                                     >  2:766435/1‑100 (MQ=255)
                                                         aaaTGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCt                                    <  2:1157937/100‑1 (MQ=255)
                                                           aTGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTa                                  <  2:1515714/100‑1 (MQ=255)
                                                           aTGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTa                                  >  1:965000/1‑100 (MQ=255)
                                                             gAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAac                                <  1:1184038/100‑1 (MQ=255)
                                                             gAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAac                                <  2:1052423/100‑1 (MQ=255)
                                                              aaGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAaca                               <  1:1045781/100‑1 (MQ=255)
                                                               aGCAAAAAGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAacac                              <  1:219871/100‑1 (MQ=255)
                                                                 cAAAAAGTAGCAAATGTAACAGTCGCGTTGACTGATCCCTGCAGTATGCATTTTACGCACCAGAGTTGATACACGTGCGATCAGCATACGCTTAACACGt                            <  2:685715/100‑1 (MQ=255)
                                                                   aaaaGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGtat                          <  1:534148/100‑1 (MQ=255)
                                                                   aaaaGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGtat                          >  1:1046637/1‑100 (MQ=255)
                                                                   aaaaGTGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGtat                          <  1:1408335/100‑1 (MQ=255)
                                                                    gatctGGCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGtata                         <  1:264437/96‑1 (MQ=255)
                                                                     aaGTGGCAAATGTAACAGTCGCGGTGGCTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTatat                        >  1:963252/1‑100 (MQ=255)
                                                                         ggtaaaTGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                    >  2:1514302/4‑100 (MQ=255)
                                                                         ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGtataagatc                    >  2:264437/1‑95 (MQ=255)
                                                                         ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                    >  1:1526/1‑100 (MQ=255)
                                                                         ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                    >  1:1405857/1‑100 (MQ=255)
                                                                         ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                    >  1:329149/1‑100 (MQ=255)
                                                                         ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                    >  2:177802/1‑100 (MQ=255)
                                                                         ggCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAgg                    >  1:574396/1‑100 (MQ=255)
                                                                          gCAAATGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGc                   >  1:1474584/1‑100 (MQ=255)
                                                                              aTGTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGGGCGATCAGCATACGCTTAACACGTATATCAGGCGGGt               <  2:1101848/100‑1 (MQ=255)
                                                                                gTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTg             <  2:648753/100‑1 (MQ=255)
                                                                                gTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTg             <  2:1046631/100‑1 (MQ=255)
                                                                                gTAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTg             <  2:1439771/100‑1 (MQ=255)
                                                                                 tAACAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGa            >  1:492697/1‑100 (MQ=255)
                                                                                  aaCAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGAc           <  2:1456692/100‑1 (MQ=255)
                                                                                  aaCAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGAc           <  1:1156672/100‑1 (MQ=255)
                                                                                  aaCAGTCGCGGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGAc           <  1:1085832/100‑1 (MQ=255)
                                                                                        cgcgGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCa     <  1:222042/100‑1 (MQ=255)
                                                                                          cgGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAAt   >  1:419892/1‑100 (MQ=255)
                                                                                          cgGTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAAt   >  1:336426/1‑100 (MQ=255)
                                                                                           ggTGACTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAATc  <  1:869986/100‑1 (MQ=255)
                                                                                                |                                                                                              
GCCCGATGCAGATCGATAACTGAAATTTTTAATTCATCTTCCCGGCCAGTAAATGGCAAATGAAGCAAAAAGTGGCAAATGTAACAGTCGCGGTGATTTATCCCTGCAGTATGCATTTTACGCACCATAGTTGCTACACGTGCGATCAGCATACGCTTAACACGTATATCAGGCGGGTTGACTGCCCAATC  >  NC_000913/3805379‑3805569

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A