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
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,067,224 C→T intergenic (‑30/+16) yihP ← / ← yihQ putative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein/putative sulpholipid alpha‑glucosidase, alpha‑glucosyl fluoride glucosidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,067,2240CT100.0% 206.9 / NA 64intergenic (‑30/+16)yihP/yihQputative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein/putative sulpholipid alpha‑glucosidase, alpha‑glucosyl fluoride glucosidase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (35/29);  total (35/29)

TATCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCCCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTCACCCGT  >  NC_000913/4067092‑4067359
                                                                                                                                    |                                                                                                                                       
tatCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                                   <  1:797966/139‑1 (MQ=255)
 atCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGc                                                                                                                                  >  1:1425986/1‑139 (MQ=255)
     agcagGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCgg                                                                                                                                <  2:641048/137‑1 (MQ=255)
     agcagGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCgg                                                                                                                                >  1:641048/1‑137 (MQ=255)
     agcagGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGAt                                                                                                                              <  1:378278/139‑1 (MQ=255)
      gcagGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGAtg                                                                                                                             <  1:1115955/139‑1 (MQ=255)
              ttAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGa                                                                                                                     <  2:109742/139‑1 (MQ=255)
              ttAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGa                                                                                                                     <  1:220963/139‑1 (MQ=255)
              ttAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGa                                                                                                                     <  1:945198/139‑1 (MQ=255)
                      cAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCttttt                                                                                                             >  2:1597370/1‑139 (MQ=255)
                         gTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAac                                                                                                          >  2:315398/1‑139 (MQ=255)
                                              tttCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCAt                                                                                     >  2:1199499/1‑139 (MQ=255)
                                                        aaGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCgg                                                                           <  1:1597370/139‑1 (MQ=255)
                                                           ggCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGgcgc                                                                        <  2:1362434/139‑1 (MQ=255)
                                                             cAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgccgcc                                                                                        >  1:712259/1‑121 (MQ=255)
                                                             cAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgccgcc                                                                                        <  2:712259/121‑1 (MQ=255)
                                                             cAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGa                                                                      >  1:576763/1‑139 (MQ=255)
                                                              aGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGgcg                                                                         >  1:382052/1‑135 (MQ=255)
                                                              aGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGgcg                                                                         <  2:382052/135‑1 (MQ=255)
                                                              aGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGAt                                                                     >  1:297476/1‑139 (MQ=255)
                                                                gCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgc                                                                                            >  2:1171032/1‑114 (MQ=255)
                                                                gCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgc                                                                                            <  1:1171032/114‑1 (MQ=255)
                                                                          gCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACcggcg                                                         >  2:606323/1‑139 (MQ=255)
                                                                           cTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACcggcgg                                                        >  2:1336214/1‑139 (MQ=255)
                                                                                  ttCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                                   <  2:1195178/57‑1 (MQ=255)
                                                                                  ttCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                                   >  1:1195178/1‑57 (MQ=255)
                                                                                  ttCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACcgg                                                           >  2:1079587/1‑129 (MQ=255)
                                                                                  ttCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACcgg                                                           <  1:1079587/129‑1 (MQ=255)
                                                                                  ttCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCg                                                 >  2:195192/1‑139 (MQ=255)
                                                                                      gTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATgg                                             >  1:82588/1‑139 (MQ=255)
                                                                                       ttGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATggg                                            <  1:606323/139‑1 (MQ=255)
                                                                                       ttGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATggg                                            <  2:576763/139‑1 (MQ=255)
                                                                                           gatgtgaCTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCa                                        <  2:3745/139‑1 (MQ=255)
                                                                                            atgtgaCTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCAt                                       >  2:267538/1‑139 (MQ=255)
                                                                                                 aCTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACg                                  >  2:698418/1‑139 (MQ=255)
                                                                                                     aTCGATGTTCTCCCTTTGCCCATGAGTTTCGTCACGGGCGGATGCGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCACATTCGCTATCGGCGCGATCAAAGACCGGCGGCTTGCCGATGGGCGCATCAACGGTaa                              >  1:1100730/1‑139 (MQ=255)
                                                                                                      tCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGgc                                                                          <  1:886476/94‑1 (MQ=255)
                                                                                                      tCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGgc                                                                          >  2:886476/1‑94 (MQ=255)
                                                                                                       cGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTAGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACt                            >  2:854525/1‑139 (MQ=255)
                                                                                                           gTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTccc                        <  1:195192/139‑1 (MQ=255)
                                                                                                            ttCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTcccc                       >  2:1293005/1‑139 (MQ=255)
                                                                                                              ctcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCa                                        <  1:1554711/120‑1 (MQ=255)
                                                                                                              ctcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCa                                        >  2:1554711/1‑120 (MQ=255)
                                                                                                               tcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGgcg                                                                         <  2:500588/86‑1 (MQ=255)
                                                                                                               tcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGgcg                                                                         >  1:500588/1‑86 (MQ=255)
                                                                                                               tcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTccccgcc                    >  1:1136050/1‑139 (MQ=255)
                                                                                                               tcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGCCGCATTAACGGTAACTTccccgcc                    >  2:743605/1‑139 (MQ=255)
                                                                                                                    ttGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACcgg                                                           <  1:380765/95‑1 (MQ=255)
                                                                                                                    ttGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACcgg                                                           >  2:380765/1‑95 (MQ=255)
                                                                                                                      gCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAAc             >  2:581966/1‑139 (MQ=255)
                                                                                                                      gCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAAc             >  1:1318361/1‑139 (MQ=255)
                                                                                                                      gCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAAc             >  1:1598785/1‑139 (MQ=255)
                                                                                                                           tGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCAtt                                                                                    >  2:102540/1‑63 (MQ=255)
                                                                                                                           tGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCAtt                                                                                    <  1:102540/63‑1 (MQ=255)
                                                                                                                             aGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTCAc      <  2:297476/139‑1 (MQ=255)
                                                                                                                             aGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTCAc      <  1:854525/139‑1 (MQ=255)
                                                                                                                             aGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTCAc      <  1:698418/139‑1 (MQ=255)
                                                                                                                               tttCCTCACGGGCGGATGTGATTAGATGCTTTTTa                                                                                                            <  1:989135/35‑1 (MQ=255)
                                                                                                                               attCCTCACGGGCGGATGTGATTAGATGCTTTTTa                                                                                                            >  2:989135/2‑35 (MQ=255)
                                                                                                                                 tCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTg                                                    >  2:1277110/1‑89 (MQ=255)
                                                                                                                                 tCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTg                                                    <  1:1277110/89‑1 (MQ=255)
                                                                                                                                 tCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTcc                         <  2:1295832/116‑1 (MQ=255)
                                                                                                                                 tCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTCACCCGt  >  2:533876/1‑139 (MQ=255)
                                                                                                                                 tCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTCACCCGt  >  1:1180591/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                       
TATCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCCCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTCACCCGT  >  NC_000913/4067092‑4067359

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A