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 F1 I2 R1 777 59.2 2955938 92.5% 2734242 106.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,862,518 Δ1 bp pseudogene (1086/1617 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_0009133,862,5160C.100.0% 227.4 / NA 54pseudogene (1088/1617 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 . (26/28);  total (26/28)

AGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACC  >  NC_000913/3862378‑3862644
                                                                                                                                          |                                                                                                                                
aGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGc                                                                                                                                  >  2:1377872/1‑139 (MQ=255)
aGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGc                                                                                                                                  >  2:835934/1‑139 (MQ=255)
  aaTCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGcca                                                                                                                                >  2:39327/1‑138 (MQ=255)
      aGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGtt                                                                                                                           <  2:305429/139‑1 (MQ=255)
       gtgtGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTc                                                                                                                          >  2:1057221‑M1/1‑138 (MQ=255)
            cGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccac                                                                                                                     <  2:719001‑M1/139‑7 (MQ=255)
                aaaCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCATCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacacca                                                                                                                 <  1:1022546‑M1/139‑11 (MQ=255)
                 aaCCACGAAGTACAGCAGTGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccactccaa                                                                                                                >  2:968268‑M1/1‑128 (MQ=255)
                  aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACTTCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaa                                                                                                               <  2:630367‑M1/139‑13 (MQ=255)
                  aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaa                                                                                                               <  2:1416168‑M1/139‑13 (MQ=255)
                  aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaa                                                                                                               <  1:1377872‑M1/139‑13 (MQ=255)
                  aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcacc                                                                                                                       <  2:760428‑M1/131‑5 (MQ=255)
                  aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcacc                                                                                                                       >  1:760428‑M1/1‑127 (MQ=255)
                     aCGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagag                                                                                                            <  1:835934‑M1/139‑16 (MQ=255)
                              agcagGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGtt                                                                                                                           <  2:771817/115‑1 (MQ=255)
                              agcagGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGtt                                                                                                                           >  1:771817/1‑115 (MQ=255)
                                   ggTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcg                                                                                              >  2:90716‑M1/1‑110 (MQ=255)
                                     tAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgac                                                                                            >  1:1441281‑M1/1‑108 (MQ=255)
                                             aaCCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                                              >  2:1218662‑M1/1‑100 (MQ=255)
                                             aaCCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                                              <  1:1218662‑M1/113‑14 (MQ=255)
                                             aaCCCAATGGCGATTTGGGTCAGCACCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggc                                                                                    >  2:909178‑M1/1‑100 (MQ=255)
                                               cccAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccg                                                                                  >  2:823425‑M1/1‑98 (MQ=255)
                                                      gCGATTTGGGTCAGCACCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccaacac                                                                           <  1:909178‑M1/139‑49 (MQ=255)
                                                         aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggc                                                                        >  2:71626‑M1/1‑88 (MQ=255)
                                                         aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggc                                                                        <  2:380559‑M1/139‑52 (MQ=255)
                                                          tttGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagc                                                                             >  1:658316‑M1/1‑87 (MQ=255)
                                                          tttGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagc                                                                             <  2:658316‑M1/133‑47 (MQ=255)
                                                                   gCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagtacggcgtgtaccgca                                                              <  1:90716‑M1/139‑62 (MQ=255)
                                                                   gCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgca                                                              <  1:190489‑M1/139‑62 (MQ=255)
                                                                         tatCCGCGTGGTTGCGGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagaggtacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagc                                                        >  1:982411‑M1/1‑72 (MQ=255)
                                                                                gTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGccat                                                                                                                               >  2:1166453/1‑60 (MQ=255)
                                                                                gTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGccat                                                                                                                               <  1:1166453/62‑3 (MQ=255)
                                                                                 tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                                              >  2:1371943‑M1/1‑64 (MQ=255)
                                                                                 tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                                              <  1:1371943‑M1/77‑14 (MQ=255)
                                                                                   gTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaa                                              >  2:428007‑M1/1‑62 (MQ=255)
                                                                                   gTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagc                                                                             <  1:367676‑M1/108‑47 (MQ=255)
                                                                                   gTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagc                                                                             >  2:367676‑M1/1‑62 (MQ=255)
                                                                                       cTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaa                                          <  2:1146818‑M1/139‑82 (MQ=255)
                                                                                       cTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaa                                          <  1:71626‑M1/139‑82 (MQ=255)
                                                                                           aCATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacagg                                      <  2:982411‑M1/139‑86 (MQ=255)
                                                                                                 ggATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgca                                                              >  2:465943‑M1/1‑48 (MQ=255)
                                                                                                 ggATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgca                                                              <  1:465943‑M1/109‑62 (MQ=255)
                                                                                                       aGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattcc                          >  1:1233959‑M1/1‑42 (MQ=255)
                                                                                                            tGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcgg                     <  2:1233959‑M1/139‑103 (MQ=255)
                                                                                                            tGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAgaga                                                                                                        <  2:388201/53‑1 (MQ=255)
                                                                                                            tGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAgaga                                                                                                        >  1:388201/1‑53 (MQ=255)
                                                                                                              cGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagc                                                                             <  2:436929‑M1/81‑47 (MQ=255)
                                                                                                              cGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagc                                                                             >  1:436929‑M1/1‑35 (MQ=255)
                                                                                                              cGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAGAGATa                                                                                                      >  2:382579/1‑53 (MQ=255)
                                                                                                              cGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAGAGATa                                                                                                      <  1:382579/53‑1 (MQ=255)
                                                                                                                   aaaCTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgcc                                                                                <  2:149049‑M1/73‑44 (MQ=255)
                                                                                                                   aaaCTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgcc                                                                                >  1:149049‑M1/1‑30 (MQ=255)
                                                                                                                   aaaCTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAag                                                                                                           >  1:311744/1‑43 (MQ=255)
                                                                                                                   aaaCTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAag                                                                                                           <  2:311744/43‑1 (MQ=255)
                                                                                                                          gTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcggttcggtaattccca       >  2:505033‑M1/1‑23 (MQ=255)
                                                                                                                             aaTCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcggttcggtaattcccacca    >  1:1041564‑M1/1‑20 (MQ=255)
                                                                                                                               tCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcggttcggtaattcccaccagc  >  1:1360481‑M1/1‑18 (MQ=255)
                                                                                                                               tCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacg                                                                          >  1:854402‑M1/1‑18 (MQ=255)
                                                                                                                               tCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacg                                                                          <  2:854402‑M1/67‑50 (MQ=255)
                                                                                                                                          |                                                                                                                                
AGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACC  >  NC_000913/3862378‑3862644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A