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
A2 F1 I1 R1 748 32.0 1685426 92.6% 1560704 103.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 376,245 (G)5→6 coding (787/1212 nt) mhpT → 3‑hydroxyphenylpropionic transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913376,2401.G100.0% 201.1 / NA 55M261R (ATG→AGG) mhpT3‑hydroxyphenylpropionic transporter
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (29/26);  total (29/26)

TGTGTTATTTCTTCACTCTGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAAT‑GGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCTTGGAACGGTGTCGTCATTTAA  >  NC_000913/376123‑376369
                                                                                                                      |                                                                                                                                 
tgtgTTATTTCTTCACTCTGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGt                                                                                                               >  2:248909/1‑139 (MQ=255)
 gtgtTATTTCTTCACTCTGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGtt                                                                                                              >  2:75092/1‑139 (MQ=255)
   gtTATTTCTTCACTCTGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTaa                                                                                                            >  1:569691/1‑139 (MQ=255)
                tctGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCAtt                                                                                               >  1:171999/1‑139 (MQ=255)
                tctGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCAtt                                                                                               <  2:360411/139‑1 (MQ=255)
                    ctgGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATg                                                                                           >  2:152003/1‑139 (MQ=255)
                          gtCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    >  1:651141/1‑108 (MQ=255)
                          gtCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    <  2:651141/108‑1 (MQ=255)
                          gtCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGa                                                                                             <  2:331704/131‑1 (MQ=255)
                          gtCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGa                                                                                             >  1:331704/1‑131 (MQ=255)
                          gtCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAg                                                                                     >  2:281506/1‑139 (MQ=255)
                          gtCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAg                                                                                     <  1:75092/139‑1 (MQ=255)
                            cTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCt                                                                                   >  2:73832/1‑139 (MQ=255)
                             tACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTg                                                                                  >  1:190977/1‑139 (MQ=255)
                             tACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTg                                                                                  <  1:152003/139‑1 (MQ=255)
                                     gATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    >  2:138966/1‑97 (MQ=255)
                                     gATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    <  1:138966/97‑1 (MQ=255)
                                     gATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCAtt                                                                                               <  2:716227/118‑1 (MQ=255)
                                     gATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCAtt                                                                                               >  1:716227/1‑118 (MQ=255)
                                     gATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGa                                                                                             >  2:698035/1‑120 (MQ=255)
                                     gATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGa                                                                                             <  1:698035/120‑1 (MQ=255)
                                       tCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTaa                                                                        >  1:673430/1‑139 (MQ=255)
                                           cTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCAt                                                                    >  2:651311/1‑139 (MQ=255)
                                              gCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    >  2:381047/1‑88 (MQ=255)
                                              gCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    <  1:381047/88‑1 (MQ=255)
                                                   cGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTAc                                                            <  1:281506/139‑1 (MQ=255)
                                                     cTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGTAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTg                                                          >  2:581840/1‑139 (MQ=255)
                                                             ggtggAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    >  1:476556/1‑73 (MQ=255)
                                                             ggtggAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    <  2:476556/73‑1 (MQ=255)
                                                             ggtggAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCa                                                                                                 >  1:157609/1‑92 (MQ=255)
                                                             ggtggAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCa                                                                                                 <  2:157609/92‑1 (MQ=255)
                                                               tggAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCg                                                <  1:249440/139‑1 (MQ=255)
                                                                ggAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGc                                                                                 <  1:263145/105‑1 (MQ=255)
                                                                ggAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGc                                                                                 >  2:263145/1‑105 (MQ=255)
                                                                 gAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGc                                              <  1:73832/139‑1 (MQ=255)
                                                                        gATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTCACCATGTCGCTACTGATTTATAGCGGCATGTTAg                                       >  1:538525/1‑139 (MQ=255)
                                                                            ccAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    <  1:333329/58‑1 (MQ=255)
                                                                            ccAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCgg                                                                                                                    >  2:333329/1‑58 (MQ=255)
                                                                            ccAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGt                                                                  <  2:531215/108‑1 (MQ=255)
                                                                            ccAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGt                                                                  >  1:531215/1‑108 (MQ=255)
                                                                                   tCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGctgctg                            <  2:190977/139‑1 (MQ=255)
                                                                                    cGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCAt                                                                                                >  2:515583/1‑70 (MQ=255)
                                                                                    cGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCAt                                                                                                <  1:515583/70‑1 (MQ=255)
                                                                                        ggcggcAGGGGTGATGTTTGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGGATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCt                       <  2:538525/139‑1 (MQ=255)
                                                                                                         ttGCCCTTCAAATGGGGGGCGGCAAGCGTGACGTTAATGTTAGGCGCATTGATGGATAAGCGGCGTCCAGTAACCATGTCGCTACTAATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCTTGGAACGGTGTCGTCAt      <  2:179099/139‑1 (MQ=255)
                                                                                                          tGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTgg                                                                                                      <  2:275506/42‑1 (MQ=255)
                                                                                                          tGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTgg                                                                                                      >  1:275506/1‑42 (MQ=255)
                                                                                                          tGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGgcg                                                                                                   <  2:832777/45‑1 (MQ=255)
                                                                                                          tGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGgcg                                                                                                   >  2:693228/1‑45 (MQ=255)
                                                                                                          tGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGgcg                                                                                                   >  1:832777/1‑45 (MQ=255)
                                                                                                          tGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGgcg                                                                                                   <  1:693228/45‑1 (MQ=255)
                                                                                                          tGCCCTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCTTGGAACGGTGTCGTCAtt     <  1:651311/139‑1 (MQ=255)
                                                                                                            cccTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCtt                                    <  1:784535/106‑1 (MQ=255)
                                                                                                            cccTGCAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCtt                                    >  2:784535/1‑106 (MQ=255)
                                                                                                                 cAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCCCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCTTGGAACGGTGTCGTCATTTaa  <  2:680045/135‑1 (MQ=255)
                                                                                                                 cAAATGGGGGGCGGCAAGCGGGACGTTAATGTTGGGCCCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCTTGGAACGGTGTCGTCATTTaa  >  1:680045/1‑135 (MQ=255)
                                                                                                                      |                                                                                                                                 
TGTGTTATTTCTTCACTCTGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTACTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAAAT‑GGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCTTGGAACGGTGTCGTCATTTAA  >  NC_000913/376123‑376369

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