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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

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.C97.9% 159.1 / ‑3.4 47coding (215/1071 nt)dhaKdihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (23/23);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01

GTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑CCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCGGATCCTGATGCA  >  NC_000913/1250495‑1250756
                                                                                                                                  |                                                                                                                                     
gTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTTAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑cccc‑ccgaa                                                                                                                             >  1:549875/1‑135 (MQ=255)
  ttCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAg                                                                                                                            <  2:411796/139‑1 (MQ=255)
  ttCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAg                                                                                                                            <  1:220286/139‑1 (MQ=255)
            aGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCTGGACAGGCCCCC‑CGAAAGCATCCCCTGa                                                                                                                  <  2:847033/139‑1 (MQ=255)
             gAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATGAACTTGCATGGCGCATTCAAAGACTTTATCGGGCGTCGGTGAGGTGAAAACTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAc                                                                                                                 <  2:871382/139‑1 (MQ=255)
              aaTATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAcc                                                                                                                <  1:562974/139‑1 (MQ=255)
                   cGCCGGTGTAATTTTTGATAATGAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGatat                                                                                                           >  2:959117/1‑139 (MQ=255)
                        gtgtAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGc                                                                                                                           >  1:882100/1‑118 (MQ=255)
                        gtgtAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGc                                                                                                                           <  2:882100/118‑1 (MQ=255)
                                                 cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAcc                                                                                                                >  2:365540/1‑104 (MQ=255)
                                                 cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAcc                                                                                                                <  1:365540/104‑1 (MQ=255)
                                                 cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCAT‑‑CCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCt                                                                               <  2:59836/135‑1 (MQ=255)
                                                 cacCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCAT‑‑CCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCt                                                                               >  1:59836/1‑135 (MQ=255)
                                                  acCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCg                                                                                 <  2:637750/134‑1 (MQ=255)
                                                  acCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCg                                                                                 >  1:637750/1‑134 (MQ=255)
                                                      tCGCCGCCATCAACTTGCATGGTGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCa                                                                        >  1:801388/1‑139 (MQ=255)
                                                      tCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATccc                                                                                                                      >  2:995097/1‑93 (MQ=255)
                                                      tCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATccc                                                                                                                      <  1:995097/93‑1 (MQ=255)
                                                      tCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgccgc                                                                          <  1:185399/137‑1 (MQ=255)
                                                      tCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgccgc                                                                          >  2:185399/1‑137 (MQ=255)
                                                      tCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCa                                                                        >  1:566652/1‑139 (MQ=255)
                                                       cgccgcCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGatat                                                                                                           <  1:634709/103‑1 (MQ=255)
                                                       cgccgcCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGatat                                                                                                           >  2:634709/1‑103 (MQ=255)
                                                       cgccgcCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgc                                                                             >  1:1220118/1‑133 (MQ=255)
                                                       cgccgcCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTgc                                                                             <  2:1220118/133‑1 (MQ=255)
                                                         ccgccATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGa                                                                                                                  >  1:1268016/1‑94 (MQ=255)
                                                         ccgccATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGa                                                                                                                  <  2:1268016/94‑1 (MQ=255)
                                                              aTCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACca                                                                                                      >  1:846957/1‑101 (MQ=255)
                                                              aTCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGAcag                                                                >  1:144681/1‑139 (MQ=255)
                                                              aTCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑CCCCACGAAAGCATCCCCTGACCGATATAACca                                                                                                      <  2:846957/101‑1 (MQ=255)
                                                                  aCTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAgg                                                            >  2:1200063/1‑139 (MQ=255)
                                                                            cgcATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAcc                                                                                                                >  2:885689/1‑77 (MQ=255)
                                                                            cgcATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAcc                                                                                                                <  1:885689/77‑1 (MQ=255)
                                                                                  cAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCAt                                                                                              <  1:1016595/89‑1 (MQ=255)
                                                                                  cAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCAt                                                                                              >  2:1016595/1‑89 (MQ=255)
                                                                                           tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAcc                                                                                                                <  2:1010622/62‑1 (MQ=255)
                                                                                           tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGAcc                                                                                                                >  1:1010622/1‑62 (MQ=255)
                                                                                           tATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCAt                                   >  1:678755/1‑139 (MQ=255)
                                                                                               gggCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGc                               <  2:868642/139‑1 (MQ=255)
                                                                                                ggCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCt                              >  2:917356/1‑139 (MQ=255)
                                                                                                 gCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGCAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGAAAAAGGGGCATCAGCTc                             <  1:959117/139‑1 (MQ=255)
                                                                                                  cGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCg                            >  2:168927/1‑139 (MQ=255)
                                                                                                        tgaggtgaAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGAc                      <  1:548415/139‑1 (MQ=255)
                                                                                                         gaggtgaAAATTTCGCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACa                     <  2:144681/139‑1 (MQ=255)
                                                                                                                       gCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAgg                                                            <  2:29271/86‑1 (MQ=255)
                                                                                                                       gCCCGGACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAgg                                                            >  1:29271/1‑86 (MQ=255)
                                                                                                                           ggACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCGGATCCTGATGc   <  1:1200063/139‑1 (MQ=255)
                                                                                                                            gACAGGCCCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCGGATCCTGCTGCa  >  2:902251/1‑139 (MQ=255)
                                                                                                                                  |                                                                                                                                     
GTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑CCCC‑CGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCGGATCCTGATGCA  >  NC_000913/1250495‑1250756

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