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 760 67.6 3323148 92.7% 3080558 109.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,176,328 (T)6→5 intergenic (‑7/+22) gatZ ← / ← gatY D‑tagatose 1,6‑bisphosphate aldolase 2, subunit/D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,176,3230T.100.0% 182.0 / NA 45intergenic (‑2/+27)gatZ/gatYD‑tagatose 1,6‑bisphosphate aldolase 2, subunit/D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (23/22);  total (23/22)

GCTTCAATCAGCACTTTGCGCGTGCTGTTGCGATCAAATGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATGTTTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGACTGCAAATAATCCCGGGGATCGG  >  NC_000913/2176188‑2176444
                                                                                                                                       |                                                                                                                         
gCTTCAATCAGCACTTTGCGCGTGCTGTTGCGATCAAATGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATGtttt                                                                                                                        >  2:232664/1‑139 (MQ=255)
               ttGCGCGTGCTGTTGCGATCAAATGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGc                                                                                                        <  2:943437/139‑1 (MQ=255)
                 gcgcGTGCTGTTGCGATCAAATGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAg                                                                                                      >  1:962654/1‑139 (MQ=255)
                 gcgcGTGCTGTTGCGATCAAATGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAg                                                                                                      <  1:232664/139‑1 (MQ=255)
                   gcgTGCTGTTGCGATCAAATGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGt                                                                                                    <  2:206397/139‑1 (MQ=255)
                                  cAAATGCCAGCGCCGCTTCGACAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGCTAtgccattcc                                                                                     <  2:962654/139‑6 (MQ=255)
                                     aTGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTc                                                                                  >  1:51162/1‑139 (MQ=255)
                                          aGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGc                                                                                                        >  1:787762/1‑112 (MQ=255)
                                          aGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGc                                                                                                        <  2:787762/112‑1 (MQ=255)
                                          aGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGc                                                                             >  1:519743/1‑139 (MQ=255)
                                                             aCGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACttt                                                          <  1:1534614/139‑1 (MQ=255)
                                                                   gggCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTcac                                                    >  1:487193/1‑139 (MQ=255)
                                                                   gggCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTcac                                                    >  2:264915/1‑139 (MQ=255)
                                                                        gAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACAt                                               >  2:1594790/1‑139 (MQ=255)
                                                                         aaCAGACTGAACATATGCCGATATGTTCACCAGCGTTATGCCGGGCAATAAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATc                                              >  2:1070905/1‑139 (MQ=255)
                                                                              aCTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCa                                         <  1:1483039/139‑1 (MQ=255)
                                                                              aCTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCa                                         >  2:476153/1‑139 (MQ=255)
                                                                              aCTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCa                                         >  2:1482467/1‑139 (MQ=255)
                                                                                tGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATc                                                               >  1:507539/1‑115 (MQ=255)
                                                                                tGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATc                                                               <  2:507539/115‑1 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATGtttttcct                                                                                                                    <  1:989814/55‑4 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATGtttttcct                                                                                                                    >  2:989814/1‑52 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCaa                                                                 <  1:919185/105‑1 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCaa                                                                 >  1:200488/1‑105 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCaa                                                                 <  2:200488/105‑1 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGAttt                               >  1:1163299/1‑139 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGAttt                               >  2:973966/1‑139 (MQ=255)
                                                                                        tGCCGATATGTTCACCAGATTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCaa                                                                 >  2:919185/1‑105 (MQ=255)
                                                                                           cGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGc                            <  2:1341476/139‑1 (MQ=255)
                                                                                            gATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACt                                                            <  2:1350905/106‑1 (MQ=255)
                                                                                            gATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACt                                                            >  1:1350905/1‑106 (MQ=255)
                                                                                            gATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTcacc                                                   >  2:102111/1‑115 (MQ=255)
                                                                                            gATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTcacc                                                   <  1:102111/115‑1 (MQ=255)
                                                                                            gATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGcc                           <  1:1396409/139‑1 (MQ=255)
                                                                                              tatGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGa                         >  2:180393/1‑139 (MQ=255)
                                                                                              tatGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGa                         <  1:1482467/139‑1 (MQ=255)
                                                                                                          cTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGt                                                                                                    <  2:1460567/52‑1 (MQ=255)
                                                                                                          cTTTATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGt                                                                                                    >  1:1460567/1‑52 (MQ=255)
                                                                                                            ttATGCCGGGCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGACTGCAAATAATccc           >  1:475922/1‑139 (MQ=255)
                                                                                                                    ggCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCg                                                                                                 >  2:77789/1‑45 (MQ=255)
                                                                                                                    ggCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCg                                                                                                 <  1:77789/45‑1 (MQ=255)
                                                                                                                    ggCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGGAGCCACAATCGGCAATCACt                                                            <  2:974829/82‑1 (MQ=255)
                                                                                                                    ggCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACt                                                            >  1:974829/1‑82 (MQ=255)
                                                                                                                     gccaTTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGACTGCAAATAATCCCGGGGATCgg  <  1:148994/136‑1 (MQ=255)
                                                                                                                     gCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGACTGCAAATAATCCCGGGGATCgg  <  2:399477/139‑1 (MQ=255)
                                                                                                                     gCAATTAACGTTTTCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGACTGCAAATAATCCCGGGGATCgg  <  1:973966/139‑1 (MQ=255)
                                                                                                                                 ttCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGa                         >  2:687046/1‑104 (MQ=255)
                                                                                                                                 ttCATG‑TTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGa                         <  1:687046/104‑1 (MQ=255)
                                                                                                                                       |                                                                                                                         
GCTTCAATCAGCACTTTGCGCGTGCTGTTGCGATCAAATGCCAGCGCCGCTTCGATAACCAACGGATGGGCAGAACAGACTGAACATATGCCGATATGTTCACCAGCTTTATGCCGGGCAATTAACGTTTTCATGTTTTTTCCTTGTTAAATGGCAGGTGCGTTATGCCCTGCCCTCGCAGCCACAATCGGCAATCACTTTGCTCACCACATCGCGCATTGCGGATTTAGCCGACTGCAAATAATCCCGGGGATCGG  >  NC_000913/2176188‑2176444

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