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 F1 I2 R1 760 67.6 3323148 92.7% 3080558 109.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,521,593 C→T *295* (TAG→TAA)  xapR ← transcriptional activator of xapAB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,521,5930CT100.0% 222.3 / NA 69*295* (TAG→TAA) xapRtranscriptional activator of xapAB
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (36/33);  total (36/33)

CACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGT  >  NC_000913/2521473‑2521726
                                                                                                                        |                                                                                                                                       
cACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGcc                                                                                                                     <  2:25139/139‑1 (MQ=255)
     cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCaa                                                                                                                   <  2:259898/136‑1 (MQ=255)
     cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCaa                                                                                                                   >  1:259898/1‑136 (MQ=255)
     cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAg                                                                                                                >  1:863284/1‑139 (MQ=255)
     cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAg                                                                                                                >  1:490319/1‑139 (MQ=255)
             tGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTGTCAATGCAGCCAACAGCt                                                                                                              <  2:1390036/135‑1 (MQ=38)
             tGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTGTCAATGCAGCCAACAGCt                                                                                                              >  1:1390036/1‑135 (MQ=255)
               tAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATc                                                                                                      >  2:283841/1‑139 (MQ=255)
               tAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATc                                                                                                      >  2:265510/1‑139 (MQ=255)
               tAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATc                                                                                                      >  2:689647/1‑139 (MQ=255)
                aaaaaaGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                     <  1:283841/139‑1 (MQ=255)
                     aGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                <  2:311401/139‑1 (MQ=255)
                       cggcgtAAAGGAGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              >  2:961661/6‑139 (MQ=255)
                       cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              <  2:1288626/139‑1 (MQ=255)
                       cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGACGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              >  1:1147579/1‑139 (MQ=255)
                         cccTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTc                                                                                             >  1:481094/1‑138 (MQ=255)
                         cccTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTc                                                                                             <  2:481094/138‑1 (MQ=255)
                                    cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑tg                                                                                                                                  <  2:1221734/90‑1 (MQ=255)
                                    cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑tg                                                                                                                                  >  1:1221734/1‑90 (MQ=255)
                                        tttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    >  2:1198598/1‑132 (MQ=255)
                                        tttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    <  1:1198598/132‑1 (MQ=255)
                                        tttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             <  1:961661/139‑1 (MQ=255)
                                         ttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATa                                                                            <  2:1042600/139‑1 (MQ=255)
                                           gCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  1:265510/139‑1 (MQ=255)
                                           gCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  2:490319/139‑1 (MQ=255)
                                           gCTATCTGCGATTTGCGAAATTGCCTGACGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  2:1147579/139‑1 (MQ=255)
                                                cTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAata                                                                     <  1:689647/139‑1 (MQ=255)
                                                 tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             <  1:708920/130‑1 (MQ=255)
                                                 tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             >  2:708920/1‑130 (MQ=255)
                                                 tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                                    >  1:673952/1‑139 (MQ=255)
                                                                tGCCTGATGCGCTTCATTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGa                                                     <  1:2765/139‑1 (MQ=255)
                                                                   cTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATgc                                                  >  2:239253/1‑139 (MQ=255)
                                                                       tGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                           <  1:597566/94‑1 (MQ=255)
                                                                       tGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                           >  2:597566/1‑94 (MQ=255)
                                                                           cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAc                                                                                                                                      >  2:1427077/1‑49 (MQ=255)
                                                                           cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAc                                                                                                                                      <  1:1427077/49‑1 (MQ=255)
                                                                            ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    >  1:1096441/1‑64 (MQ=255)
                                                                            ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    <  2:1096441/64‑1 (MQ=255)
                                                                             tCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                <  1:1178039/83‑1 (MQ=255)
                                                                             tCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                >  2:1178039/1‑83 (MQ=255)
                                                                                   aGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAAtatata                                                                 >  2:498020/1‑108 (MQ=255)
                                                                                   aGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAAtatata                                                                 <  1:498020/108‑1 (MQ=255)
                                                                                     cAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgga                                <  1:239253/139‑1 (MQ=255)
                                                                                        actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCa                                                                                            <  1:1007895/76‑1 (MQ=255)
                                                                                        actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCa                                                                                            >  2:1007895/1‑76 (MQ=255)
                                                                                        actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                        >  2:1605984/1‑96 (MQ=255)
                                                                                        actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                        <  1:1605984/96‑1 (MQ=255)
                                                                                          tactaTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctgct                                                                                      >  2:522215/1‑80 (MQ=255)
                                                                                          tactaTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctgct                                                                                      <  1:522215/80‑1 (MQ=255)
                                                                                          tactaTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATg                           >  1:546491/1‑139 (MQ=255)
                                                                                             taTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    >  2:977975/1‑79 (MQ=255)
                                                                                             taTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    <  1:977975/79‑1 (MQ=255)
                                                                                             taTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGaca                        >  1:1427732/1‑139 (MQ=255)
                                                                                             taTCTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGaca                        >  1:1380465/1‑139 (MQ=255)
                                                                                               tttCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          >  2:466606/1‑87 (MQ=255)
                                                                                               tttCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  1:466606/87‑1 (MQ=255)
                                                                                               tttCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACAcc                      >  2:89237/1‑139 (MQ=255)
                                                                                                 tCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTg                    <  2:863284/139‑1 (MQ=255)
                                                                                                    ggCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGcc                 >  2:616656/1‑139 (MQ=255)
                                                                                                      cAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    >  2:1345724/1‑38 (MQ=255)
                                                                                                      cAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    <  1:1345724/38‑1 (MQ=255)
                                                                                                         ttCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgg                                 <  1:1052672/118‑1 (MQ=255)
                                                                                                         ttCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgg                                 >  2:1052672/1‑118 (MQ=255)
                                                                                                         ttCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTc            >  1:687240/1‑139 (MQ=255)
                                                                                                                   ctcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          >  2:641733/1‑67 (MQ=255)
                                                                                                                   ctcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  1:641733/67‑1 (MQ=255)
                                                                                                                   ctcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGt  >  2:1072105/1‑139 (MQ=255)
                                                                                                                    tcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATcgcg                                                                                                   >  1:942031/1‑41 (MQ=255)
                                                                                                                    tcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATcgcg                                                                                                   <  2:942031/41‑1 (MQ=255)
                                                                                                                        |                                                                                                                                       
CACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGT  >  NC_000913/2521473‑2521726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A