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
A14 F1 I2 R1 774 49.2 2112398 96.9% 2046913 118.5

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_0009133,862,4970CT98.4% 190.3 / ‑5.2 61pseudogene (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 (1/0);  new base T (30/30);  total (31/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CACATGTTGAACTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAG  >  NC_000913/3862363‑3862625
                                                                                                                                      |                                                                                                                                
cacaTGTTGAACTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGt                                                                                                                              >  1:86889/1‑139 (MQ=255)
    tGTTGAACTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAAt                                                                                                                          <  2:190297/139‑1 (MQ=255)
              cAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                >  2:204712/1‑139 (MQ=255)
              cAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCg                                                                                                                <  1:204712/139‑1 (MQ=255)
                        gtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcac                                                                                                     <  2:503680‑M1/139‑4 (MQ=255)
                        gtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTca                                                                                                      <  2:291096‑M1/138‑3 (MQ=255)
                        gtgCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTca                                                                                                      >  1:291096‑M1/1‑136 (MQ=255)
                           cGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCa                                                                                                                        <  1:780068/118‑1 (MQ=255)
                           cGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCa                                                                                                                        >  2:780068/1‑118 (MQ=255)
                           cGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccac                                                                                                  >  1:715508‑M1/1‑133 (MQ=255)
                               aaaCCACGAATTACAGCAGGGTAAAGCACAACCCAATGTCGATTTGGGTCATCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacacca                                                                                              <  2:779329‑M1/139‑11 (MQ=255)
                               aaaCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacacca                                                                                              >  2:263507‑M1/1‑129 (MQ=255)
                                 aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaa                                                                                            >  1:924395‑M1/1‑127 (MQ=255)
                                 aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaa                                                                                            <  1:776996‑M1/139‑13 (MQ=255)
                                 aCCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGATCAGCATCATATCCGCGTGGTTGCTGAACATCGGGAGCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaa                                                                                            <  2:944603‑M1/139‑13 (MQ=255)
                                     cGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCt                                                                                                                   <  2:268419/113‑1 (MQ=255)
                                     cGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCt                                                                                                                   >  1:268419/1‑113 (MQ=255)
                                         gTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagataca                                                                                    <  1:332449‑M1/139‑21 (MQ=255)
                                                    tAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTcc                                                                                                                 <  1:27023/100‑1 (MQ=255)
                                                    tAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTcc                                                                                                                 >  2:27023/1‑100 (MQ=255)
                                                    tAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgac                                                                         >  2:927875‑M1/1‑108 (MQ=255)
                                                          acaACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgag                                                                   <  1:495895‑M1/139‑38 (MQ=255)
                                                          acaACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCAGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgag                                                                   <  2:19258‑M1/139‑38 (MQ=255)
                                                            aaCCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggc                                                                 <  1:33144‑M1/139‑40 (MQ=255)
                                                              cccAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccg                                                               >  2:272985‑M1/1‑98 (MQ=255)
                                                               ccAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgc                                                              <  1:263507‑M1/139‑43 (MQ=255)
                                                                 aaTGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccagagagatacattacggtcgacattgaggccgcca                                                            >  2:855891‑M1/1‑95 (MQ=255)
                                                                        aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGccatg                                                                                                           >  2:125503/1‑83 (MQ=255)
                                                                        aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGccatg                                                                                                           <  1:125503/86‑4 (MQ=255)
                                                                        aTTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggc                                                     >  1:62579‑M1/1‑88 (MQ=255)
                                                                                  gCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgca                                           <  1:116431‑M1/139‑62 (MQ=255)
                                                                                       atatCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGcc                                                                                                              <  2:511876/68‑1 (MQ=255)
                                                                                       atatCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGcc                                                                                                              >  1:511876/1‑68 (MQ=255)
                                                                                         atCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTTCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagca                                    >  1:983979‑M1/1‑71 (MQ=255)
                                                                                             gcgTTGTTGCTGAACAACTGGATCAACTTTTGCGGGAAAACCTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCATACCCAAGAGACACATTACGGTCGACATTGAGGCCGCCTACACCCCGTCTACCACACACAGCTAccg                             >  2:88740/1‑137 (MQ=255)
                                                                                             gcgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagaga                                                                                        >  1:266541‑M1/1‑67 (MQ=255)
                                                                                             gcgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagaga                                                                                        <  2:266541‑M1/83‑17 (MQ=255)
                                                                                                tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtga                             >  1:446302‑M1/1‑64 (MQ=255)
                                                                                                tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacg                                                       <  2:106754‑M1/113‑50 (MQ=255)
                                                                                                tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacg                                                       >  1:106754‑M1/1‑64 (MQ=255)
                                                                                                tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                           <  2:979654‑M1/77‑14 (MQ=255)
                                                                                                tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaag                                                                                           >  1:979654‑M1/1‑64 (MQ=255)
                                                                                                tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcacc                                                                                                    >  2:939784‑M1/1‑64 (MQ=255)
                                                                                                tGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcacc                                                                                                    <  1:939784‑M1/68‑5 (MQ=255)
                                                                                                  gTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaa                           >  2:292077‑M1/1‑62 (MQ=255)
                                                                                                          aCATCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacagg                   <  1:76084‑M1/139‑86 (MQ=255)
                                                                                                             tCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAGAGATACAtt                                                                               >  2:1054274/1‑73 (MQ=255)
                                                                                                             tCGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAGAGATACAtt                                                                               <  1:1054274/73‑1 (MQ=255)
                                                                                                              cGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaagg               >  2:824583‑M1/1‑50 (MQ=255)
                                                                                                              cGGGATCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaagg               >  1:533952‑M1/1‑50 (MQ=255)
                                                                                                                   tCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtg                                                  <  1:942455‑M1/99‑55 (MQ=255)
                                                                                                                   tCCAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtg                                                  >  2:942455‑M1/1‑45 (MQ=255)
                                                                                                                     cAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGcc                                                                                                              >  1:945344/1‑38 (MQ=255)
                                                                                                                     cAGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCGcc                                                                                                              <  2:945344/38‑1 (MQ=255)
                                                                                                                      aGTTTTGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattcc       >  1:853355‑M1/1‑42 (MQ=255)
                                                                                                                        ttttGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccag     <  1:937106‑M1/139‑100 (MQ=255)
                                                                                                                          ttGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcg   >  1:619631‑M1/1‑38 (MQ=255)
                                                                                                                           tGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcgg  <  1:927875‑M1/139‑103 (MQ=255)
                                                                                                                           tGCGGTAAAACTTAGTCAATCAGACCTCCG‑CCATGTTcaccacaccaaagagatacattacggtcgacattgaggccgccagcacggcgtgtaccgcaaacagcaacggtgaaatgaacaggaaggtaaattccagcgg  <  1:272985‑M1/139‑103 (MQ=255)
                                                                                                                                  aaaCTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAgaga                                                                                     <  2:31311/46‑1 (MQ=255)
                                                                                                                                  aaaCTTAGTCAATCAGACCTCCG‑CCATGTT‑‑‑CACCACACCAAAgaga                                                                                     >  1:31311/1‑46 (MQ=255)
                                                                                                                                      |                                                                                                                                
CACATGTTGAACTGCAGAATCAGTGTGCGGAAAACCACGAAGTACAGCAGGGTAAAGCACAACCCAATGGCGATTTGGGTCAGCATCATATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAG  >  NC_000913/3862363‑3862625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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