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 59 52.6 2411032 94.1% 2268781 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,858,248 T→C T53A (ACG→GCG)  yidJ ← sulfatase/phosphatase superfamily protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,858,2480TC100.0% 197.6 / NA 52T53A (ACG→GCG) yidJsulfatase/phosphatase superfamily protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (28/24);  total (28/24)

TGTAACAGGTGTGATAGCCGGCATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGTACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGACCATATTGGTGGCCTGGGTATCGGTCATGACGAA  >  NC_000913/3858113‑3858383
                                                                                                                                       |                                                                                                                                       
tGTAACAGGTGTGATAGCCGGCATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGcaca                                                                                                                                      <  1:120206/139‑1 (MQ=255)
     cAGGTGTGGTAGCCGGCATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCTCGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCg                                                                                                                                 <  1:716863/139‑1 (MQ=255)
         tgtgATAGCCGGCATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAAc                                                                                                                                   >  1:483419/1‑133 (MQ=255)
         tgtgATAGCCGGCATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAAc                                                                                                                                   <  2:483419/133‑1 (MQ=255)
                   ggCATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGC‑GGCGCACAAACCGGTGAACAGGTGTAgg                                                                                                                  >  2:1187106/1‑139 (MQ=255)
                     cATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGaa                                                                                                                            <  1:695938/128‑1 (MQ=255)
                     cATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGaa                                                                                                                            >  2:695938/1‑128 (MQ=255)
                              aGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTaaa                                                                                                        <  2:1106067/139‑1 (MQ=255)
                                  gcgcCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGa                                                                                                    >  1:1008403/1‑139 (MQ=255)
                                  gcgcCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGa                                                                                                    >  1:313471/1‑139 (MQ=255)
                                   cgcCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAAc                                                                                                                                   <  2:587093/107‑1 (MQ=255)
                                   cgcCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAAc                                                                                                                                   >  1:587093/1‑107 (MQ=255)
                                   cgcCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGa                                                                                                    >  2:3318/1‑138 (MQ=255)
                                   cgcCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGa                                                                                                    <  1:3318/138‑1 (MQ=255)
                                            gTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTccg                                                                                          <  1:248616/139‑1 (MQ=255)
                                                  aTGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGC‑GGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAg                                                                                   <  1:1187106/139‑1 (MQ=255)
                                                    gTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGa                                                                                  >  1:461646/1‑139 (MQ=255)
                                                     tttttGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGAc                                                                                 <  2:1022256/139‑1 (MQ=255)
                                                               gcgcGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATAtt                                                                       >  1:1017617/1‑139 (MQ=255)
                                                                cgcgACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAatat                                                                        >  2:793810/1‑137 (MQ=255)
                                                                cgcgACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAatat                                                                        <  1:793810/137‑1 (MQ=255)
                                                                                  cGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTa                                                    >  2:905397/1‑139 (MQ=255)
                                                                                        ggACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGtt                                                      >  2:16988/1‑131 (MQ=255)
                                                                                        ggACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGtt                                                      <  1:16988/131‑1 (MQ=255)
                                                                                          aCTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATc                                                                             >  1:1191148/1‑106 (MQ=255)
                                                                                          aCTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATc                                                                             <  2:1191148/106‑1 (MQ=255)
                                                                                               ttAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAAc                                       >  1:558189/1‑139 (MQ=255)
                                                                                                tAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAAcc                                      <  1:905397/139‑1 (MQ=255)
                                                                                                tAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAAcc                                      <  2:213956/139‑1 (MQ=255)
                                                                                                        aTACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAGCAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGa                                    <  1:766596/133‑1 (MQ=255)
                                                                                                        aTACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCTGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGa                                    >  2:766596/1‑133 (MQ=255)
                                                                                                        aTACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGACCatat                              >  2:1074026/1‑139 (MQ=255)
                                                                                                        aTACCGGTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGACCatat                              >  2:1173914/1‑139 (MQ=255)
                                                                                                             ggTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGaa                                                                                                                            <  2:1162541/40‑1 (MQ=255)
                                                                                                             ggTAAATAGTCCGGCCCGTGCAGGCGCACAAACCGGTGaa                                                                                                                            >  1:1162541/1‑40 (MQ=255)
                                                                                                                aaaTAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGTGGTTTACCGCTATAGCAACCGACCATATTGGTGGcc                      <  2:564901/139‑1 (MQ=255)
                                                                                                                  aTAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAg                                                                                   <  2:1198073/76‑1 (MQ=255)
                                                                                                                  aTAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAg                                                                                   >  1:1198073/1‑76 (MQ=255)
                                                                                                                  aTAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAg                                           >  1:497852/1‑116 (MQ=255)
                                                                                                                  aTAGTCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAg                                           <  2:497852/116‑1 (MQ=255)
                                                                                                                      tCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGAc                                                                                 <  1:9031/74‑1 (MQ=255)
                                                                                                                      tCCGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGAc                                                                                 >  2:9031/1‑74 (MQ=255)
                                                                                                                      tCCGGCCCGGGCAGGCGCACACACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGAACATATTGGTGGCCTGGGTa                >  2:729872/1‑139 (MQ=255)
                                                                                                                        cGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTAcc                                                  >  2:126531/1‑103 (MQ=255)
                                                                                                                        cGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTAcc                                                  <  1:126531/103‑1 (MQ=255)
                                                                                                                        cGGCCCGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGACCATATTGGTGGCCTGGGTATc              >  2:928777/1‑139 (MQ=255)
                                                                                                                           cccGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTc                                                                                            <  2:638872/58‑1 (MQ=255)
                                                                                                                           cccGTGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTc                                                                                            >  1:638872/1‑58 (MQ=255)
                                                                                                                               tGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTAtt                                                              <  1:1203453/84‑1 (MQ=255)
                                                                                                                               tGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTAtt                                                              >  2:1203453/1‑84 (MQ=255)
                                                                                                                               tGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAAcc                                      >  2:433979/1‑108 (MQ=255)
                                                                                                                               tGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAAcc                                      <  1:433979/108‑1 (MQ=255)
                                                                                                                               tGCAGGCGCACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGACCATATTGGTGGCCTGGGTATCGGTCATg       >  2:568673/1‑139 (MQ=255)
                                                                                                                                    gcgcACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGACCATATTGGTGGCCTGGGTATCGGTCATGACGaa  <  1:588800/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
TGTAACAGGTGTGATAGCCGGCATCCTTAAAGTAGCGCCCCATAGTGGAGATGTTTTTGCCTGGCGCGACGTTGTTGGTCCACGGGCCGGACTGGTTAGCGTAGATACCGGTAAATAGTCCGGCCCGTGCAGGCGTACAAACCGGTGAACAGGTGTAGGCGGAATTAAAGCGAATACCTTCCGCCGCCAGACTATCAATATTTTGCGTATTCAGCGGTTTACCGCTATAGCAACCGACCATATTGGTGGCCTGGGTATCGGTCATGACGAA  >  NC_000913/3858113‑3858383

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