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 1,250,629 (C)5→6 coding (210/1071 nt) dhaK ← dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,250,6241.C95.8% 158.6 / ‑0.3 48coding (215/1071 nt)dhaKdihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (19/27);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GGTCGCTGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑C‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCGGATCCTGATG  >  NC_000913/1250488‑1250754
                                                                                                                                          |                                                                                                                                   
ggTCGCTGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c‑c                                                                                                                                  >  1:790302/1‑139 (MQ=255)
  tCGCTGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c‑ccc                                                                                                                                >  1:708101/1‑139 (MQ=255)
                   cgAATATCGCCGGTGTAATTTTTGATAATGAACAGTACACCTTCGCCGCCATCAGCGTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGa                                                                                                                <  1:55292/138‑1 (MQ=255)
                   aGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGa                                                                                                                <  2:137026/139‑1 (MQ=255)
                   aGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑CTCCCCGAAAGCATCCCCTGa                                                                                                                <  1:792594/139‑1 (MQ=255)
                     aaTATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              <  2:708101/139‑1 (MQ=255)
                     aaTATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              <  2:550406/139‑1 (MQ=255)
                         tCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGata                                                                                                          <  2:361605/139‑1 (MQ=255)
                                                      tACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCt                                                                             >  2:825582/1‑139 (MQ=255)
                                                        cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGc                                                                                                                         <  2:936538/93‑1 (MQ=255)
                                                        cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGc                                                                                                                         >  1:936538/1‑93 (MQ=255)
                                                        cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgc                                                                           >  2:1373144/1‑139 (MQ=255)
                                                        cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgc                                                                           >  1:1291608/1‑139 (MQ=255)
                                                        cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c                                                                                                                                    >  2:1173277/1‑82 (MQ=255)
                                                        cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c                                                                                                                                    <  1:1173277/82‑1 (MQ=255)
                                                         acCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgcc                                                                          >  2:1093357/1‑139 (MQ=255)
                                                          ccTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGAC‑C‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgccg                                                                         >  1:263408/1‑139 (MQ=255)
                                                           cTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              >  2:1114866/1‑101 (MQ=255)
                                                           cTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              <  1:1114866/101‑1 (MQ=255)
                                                             tCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACca                                                                                                    <  1:319521/109‑1 (MQ=255)
                                                             tCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACca                                                                                                    >  2:319521/1‑109 (MQ=255)
                                                              cgccgcCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGc                                                                                                                         >  1:19358/1‑87 (MQ=255)
                                                              cgccgcCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGc                                                                                                                         <  2:19358/87‑1 (MQ=255)
                                                                ccgccATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCAccc                                                                   >  2:1024121/1‑139 (MQ=255)
                                                                              cATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGAc                                                     >  2:1123212/1‑139 (MQ=255)
                                                                                   cgcATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTc                                                >  1:743453/1‑139 (MQ=255)
                                                                                    gcATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTcc                                               <  1:1024121/139‑1 (MQ=255)
                                                                                    gcATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTcc                                               >  2:32166/1‑139 (MQ=255)
                                                                                    gcATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTcc                                               <  2:261929/139‑1 (MQ=255)
                                                                                     cATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              <  2:565949/75‑1 (MQ=255)
                                                                                     cATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              >  1:565949/1‑75 (MQ=255)
                                                                                        tCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c‑cccccg                                                                                                                             >  2:1414988/1‑54 (MQ=255)
                                                                                        tCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c‑cccccg                                                                                                                             <  1:1414988/56‑3 (MQ=255)
                                                                                             gATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAgg                                      <  1:825582/139‑1 (MQ=255)
                                                                                                  tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCAt                                 >  1:382396/1‑139 (MQ=255)
                                                                                                  tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCAt                                 >  1:354576/1‑139 (MQ=255)
                                                                                                  tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c                                                                                                                                    <  1:521525/40‑1 (MQ=255)
                                                                                                  tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c                                                                                                                                    >  2:1366568/1‑40 (MQ=255)
                                                                                                  tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c                                                                                                                                    >  2:521525/1‑40 (MQ=255)
                                                                                                  tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑c                                                                                                                                    <  1:1366568/40‑1 (MQ=255)
                                                                                                      gggCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGc                             <  1:1093357/139‑1 (MQ=255)
                                                                                                      gggCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGc                             <  2:354576/139‑1 (MQ=255)
                                                                                                       ggCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCt                            <  2:263408/139‑1 (MQ=255)
                                                                                                        gCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGCCCGatat                                                                                                         >  2:1087749/1‑61 (MQ=255)
                                                                                                        gCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGatat                                                                                                         <  1:1087749/61‑1 (MQ=255)
                                                                                                        gCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTc                           >  2:600466/1‑139 (MQ=255)
                                                                                                        gCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTc                           <  2:382396/139‑1 (MQ=255)
                                                                                                          gTCGGTGAGGTGAAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCgg                         <  1:1373144/139‑1 (MQ=255)
                                                                                                               tgaggtgaAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGAc                    <  1:600466/139‑1 (MQ=255)
                                                                                                                  ggtgaAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAAc                                                                                                      <  1:117957/54‑1 (MQ=255)
                                                                                                                  ggtgaAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAAc                                                                                                      >  2:117957/1‑54 (MQ=255)
                                                                                                                  ggtgaAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATa                 <  1:32166/139‑1 (MQ=255)
                                                                                                                    tgaAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              >  2:1016059/1‑44 (MQ=255)
                                                                                                                    tgaAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGAcc                                                                                                              <  1:1016059/44‑1 (MQ=255)
                                                                                                                    tgaAAATTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATaca               <  2:743453/139‑1 (MQ=255)
                                                                                                                       aaaTTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCg            <  1:59663/139‑1 (MQ=255)
                                                                                                                       aaaTTTCGCCCGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCg            <  2:1137983/139‑1 (MQ=255)
                                                                                                                                 cGGACAG‑GCC‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCGGATCCTGATg  <  2:1240715/139‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                   
GGTCGCTGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAG‑G‑C‑CCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCGGATCCTGATG  >  NC_000913/1250488‑1250754

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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