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 I1 R1 300 54.7 1718999 98.4% 1691495 149.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,048,639 G→A P18L (CCC→CTC)  gfcC ← putative O‑antigen capsule production periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,048,6390GA100.0% 210.6 / NA 56P18L (CCC→CTC) gfcCputative O‑antigen capsule production periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/30);  total (26/30)

GTCGGTCAGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAACCTGGCCAGTAGCCG  >  NC_000913/1048491‑1048776
                                                                                                                                                    |                                                                                                                                         
gTCGGTCAGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAgt                                                                                                                                         <  2:370339/151‑1 (MQ=255)
  cGGTCAGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAgtgt                                                                                                                                       <  2:241736/151‑1 (MQ=255)
  cGGTCAGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAgtg                                                                                                                                        <  2:827596/150‑1 (MQ=255)
   ggTCAGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTc                                                                                                                                      >  2:123829/1‑151 (MQ=255)
   ggTCAGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTc                                                                                                                                      >  1:326034/1‑151 (MQ=255)
       aGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCAtt                                                                                                                                   >  2:721526/1‑150 (MQ=255)
        gCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTAc                                                                                                                                 <  2:608288/151‑1 (MQ=255)
           aGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTa                                                                                                                              <  1:645992/151‑1 (MQ=255)
            ggCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTaa                                                                                                                             <  1:761906/151‑1 (MQ=255)
             gCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTaaa                                                                                                                            <  1:624916/151‑1 (MQ=255)
             gCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTaa                                                                                                                             >  1:682008/1‑150 (MQ=255)
               aCCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAg                                                                                                                           >  1:735686/1‑150 (MQ=255)
                      caccaGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTgg                                                                                                                   <  2:357381/151‑1 (MQ=255)
                        ccaGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCa                                                                                                                 <  2:399465/151‑1 (MQ=255)
                         caGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCa                                                                                                                 >  2:849061/1‑150 (MQ=255)
                           gagGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATg                                                                                                              <  2:58050/151‑1 (MQ=255)
                               cGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAAt                                                                                                          >  2:830477/1‑151 (MQ=255)
                                gATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAAt                                                                                                          >  1:362055/1‑150 (MQ=255)
                                gATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATa                                                                                                         <  2:571093/151‑1 (MQ=255)
                                    gcgcAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGAc                                                                                                     >  1:775671/1‑151 (MQ=255)
                                         gTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTaa                                                                                                <  1:256305/151‑1 (MQ=255)
                                         gTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTaa                                                                                                <  2:698338/151‑1 (MQ=255)
                                            gCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAAttt                                                                                             <  1:632860/151‑1 (MQ=255)
                                            gCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAAtt                                                                                              <  1:645708/150‑1 (MQ=255)
                                            gCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAAtt                                                                                              <  1:343092/150‑1 (MQ=255)
                                               gTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTAtt                                                                                          <  2:552222/151‑1 (MQ=255)
                                               gTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTAtt                                                                                          >  2:154092/1‑151 (MQ=255)
                                                 tgtgTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTc                                                                                         <  2:856031/150‑1 (MQ=255)
                                                      cACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGt                                                                                    <  2:121195/150‑1 (MQ=255)
                                                       aCCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATATGACTGTAATTTATTCATGGTGc                                                                                  <  2:447937/151‑1 (MQ=255)
                                                              ggACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTa                                                                           <  2:221489/151‑1 (MQ=255)
                                                                 caacaTTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGa                                                                        <  2:326057/151‑1 (MQ=255)
                                                                       tttCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGt                                                                   <  1:258741/150‑1 (MQ=255)
                                                                         tCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCAt                                                                >  1:307658/1‑151 (MQ=255)
                                                                            aCGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTc                                                             <  1:263122/151‑1 (MQ=255)
                                                                             cGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCt                                                            <  1:705969/151‑1 (MQ=255)
                                                                              ggggCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCt                                                            >  1:355529/1‑150 (MQ=255)
                                                                              ggggCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCt                                                            >  1:441117/1‑150 (MQ=255)
                                                                                 gCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCGTTTCTACgg                                                        >  2:791853/1‑151 (MQ=255)
                                                                                 gCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACgg                                                        <  2:494871/151‑1 (MQ=255)
                                                                                    aaCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGa                                                      >  1:719821/1‑150 (MQ=255)
                                                                                    aaCGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGa                                                      >  1:838060/1‑150 (MQ=255)
                                                                                        gAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAAc                                                 >  1:841369/1‑151 (MQ=255)
                                                                                         aaaGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAAcc                                                >  2:84227/1‑151 (MQ=255)
                                                                                            gtgtCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCt                                             <  2:364240/151‑1 (MQ=255)
                                                                                                    tgttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTa                                      <  1:759046/150‑1 (MQ=255)
                                                                                                     gttCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAAc                                    <  2:441151/151‑1 (MQ=255)
                                                                                                        cGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACAtt                                 >  1:746917/1‑151 (MQ=255)
                                                                                                                aGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACt                         >  1:265771/1‑151 (MQ=255)
                                                                                                                  aTAAATAGTCACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACttt                       >  2:26391/1‑151 (MQ=255)
                                                                                                                           cACCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAAcc               <  1:566150/150‑1 (MQ=255)
                                                                                                                            aCCGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAACCTg             >  2:690917/1‑151 (MQ=255)
                                                                                                                              cGTTCCTTGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAACCTGGc           >  1:703819/1‑151 (MQ=255)
                                                                                                                                    ttGCGCAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAACCTGGCCa         >  1:558586/1‑147 (MQ=255)
                                                                                                                                        gcAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAACCTGGCCAGTAGCCg  >  2:777382/1‑150 (MQ=255)
                                                                                                                                        gcAAAGGCATGGAGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAACCTGGCCAGTAGCCg  >  2:94820/1‑150 (MQ=255)
                                                                                                                                                    |                                                                                                                                         
GTCGGTCAGCAAGGCACCAGGCCACCAGAGGCGATCGCGCAGTTGCGGTTGTGTCACCAACTGGACAACATTTTCCACGGGGCCAACGGAAAGTGTCTGTTGTTCGCCAGGCAGATAAATAGTCACCGTTCCTTGCGCAAAGGCATGGGGTGTCATTACGTAAAGTACGCTGGCAATGAAATACGACTGTAATTTATTCATGGTGCGGGTTTAAGAAACGTCATTTCTACGGGAATAACCCCTGCGCCTAACATTTGCCGACTTTGACGAACCTGGCCAGTAGCCG  >  NC_000913/1048491‑1048776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A