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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,862,497 C→T pseudogene (1107/1617 nt) glvC ← pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,862,4970CT100.0% 184.0 / NA 57pseudogene (1107/1617 nt)glvCpseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/30);  total (27/30)

CACATGTTGAACTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCG  >  NC_000913/3862363‑3862627
                                                                                                                                      |                                                                                                                                  
cacaTGTTGAACTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGt                                                                                                                                >  1:1341333/1‑139 (MQ=255)
         aaCTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAg                                                                                                                                 >  2:130421/1‑129 (MQ=255)
         aaCTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAg                                                                                                                                 <  1:130421/129‑1 (MQ=255)
           cTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCt                                                                                                                     <  1:1247688/139‑1 (MQ=255)
             gCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGTGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGAccctg                                                                                                                   >  2:292604/1‑136 (MQ=255)
              cAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCGGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                  >  2:239151/1‑139 (MQ=255)
              cAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                  <  2:20928/139‑1 (MQ=255)
              cAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                  >  2:1180250/1‑139 (MQ=255)
              cAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                  >  2:731401/1‑139 (MQ=255)
              cAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                  >  2:1071763/1‑139 (MQ=255)
               aGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGc                                                                                                                 >  1:69562/1‑139 (MQ=255)
                  aTCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGccat                                                                                                              <  2:1341333/139‑3 (MQ=255)
                   tCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGTGGTAAAACTTAGTCAATCAGACCTCCGccatg                                                                                                             <  2:966943/139‑4 (MQ=255)
                       tgtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGTGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGAccctgtctcttatac                                                                                                         <  1:292604/139‑14 (MQ=255)
                       tgtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTca                                                                                                        <  1:1180250‑M1/139‑3 (MQ=255)
                        gtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                  <  2:1238546/129‑1 (MQ=255)
                        gtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                  >  1:1238546/1‑129 (MQ=255)
                        gtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcac                                                                                                       <  2:1211708‑M1/139‑4 (MQ=255)
                           cGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCa                                                                                                                          >  1:69386/1‑118 (MQ=255)
                           cGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCa                                                                                                                          <  2:69386/118‑1 (MQ=255)
                               aaaCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacacca                                                                                                <  1:731401‑M1/139‑11 (MQ=255)
                               aaaCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacacca                                                                                                <  2:69562‑M1/139‑11 (MQ=255)
                                 aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCGGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaa                                                                                              <  1:239151‑M1/139‑13 (MQ=255)
                                     cGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTCAACATCGGGATCCAGTTTTGCGGTAAATCTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagg                                                                                          <  2:1225629‑M1/139‑17 (MQ=255)
                                           aCAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacatt                                                                                    <  2:172607‑M1/139‑23 (MQ=255)
                                             agcagGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattac                                                                                  >  1:622870‑M1/1‑115 (MQ=255)
                                                    tAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAg                                                                                                                                 <  2:166016/86‑1 (MQ=255)
                                                    tAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAg                                                                                                                                 >  1:166016/1‑86 (MQ=255)
                                                         cacaACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTca                                                                                                        <  1:1122836‑M1/105‑3 (MQ=255)
                                                         cacaACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTca                                                                                                        >  2:1122836‑M1/1‑103 (MQ=255)
                                                              cccAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccg                                                                 <  2:622870‑M1/139‑42 (MQ=255)
                                                              cccAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcac                                                                                                       >  1:1070567‑M1/1‑98 (MQ=255)
                                                              cccAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcac                                                                                                       <  2:1070567‑M1/101‑4 (MQ=255)
                                                                        aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacac                                                                                                  >  2:1087572‑M1/1‑88 (MQ=255)
                                                                        aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacac                                                                                                  <  1:1087572‑M1/96‑9 (MQ=255)
                                                                        aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTca                                                                                                        >  2:302338‑M1/1‑88 (MQ=255)
                                                                        aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTca                                                                                                        <  1:302338‑M1/90‑3 (MQ=255)
                                                                          ttGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGAc                                                                                                                       <  2:355198/74‑1 (MQ=255)
                                                                          ttGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGAc                                                                                                                       >  1:355198/1‑74 (MQ=255)
                                                                                        tatCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagc                                       >  2:121568‑M1/1‑72 (MQ=255)
                                                                                             gcgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacgg                                  >  2:480198‑M1/1‑67 (MQ=255)
                                                                                              cgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                             <  2:367893‑M1/79‑14 (MQ=255)
                                                                                              cgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                             >  1:367893‑M1/1‑66 (MQ=255)
                                                                                                 ggTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaa                              <  1:1071763‑M1/139‑77 (MQ=255)
                                                                                                     gCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacatta                                                                                   >  2:257472‑M1/1‑59 (MQ=255)
                                                                                                     gCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacatta                                                                                   <  1:257472‑M1/82‑24 (MQ=255)
                                                                                                         aaCATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacag                      <  1:480198‑M1/139‑85 (MQ=255)
                                                                                                              cGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaagg                 >  1:11160‑M1/1‑50 (MQ=255)
                                                                                                              cGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacac                                                                                                  <  1:867300/58‑3 (MQ=255)
                                                                                                              cGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacac                                                                                                  >  2:867300/1‑56 (MQ=255)
                                                                                                                ggATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggta               >  2:633261‑M1/1‑48 (MQ=255)
                                                                                                                          ttGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccag       >  1:81858‑M1/1‑38 (MQ=255)
                                                                                                                          ttGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccag       <  2:81858‑M1/137‑100 (MQ=255)
                                                                                                                           tGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcgg    <  1:121568‑M1/139‑103 (MQ=255)
                                                                                                                             cGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcggtt  >  1:1213842‑M1/1‑35 (MQ=255)
                                                                                                                             cGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAag                                                                                          >  1:981241/1‑48 (MQ=255)
                                                                                                                             cGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAag                                                                                          <  2:981241/48‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                  
CACATGTTGAACTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCG  >  NC_000913/3862363‑3862627

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