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
A22 F64 I1 R1 18 58.3 2092080 92.1% 1926805 145.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA3,560,4551.G95.9% 132.4 / ‑1.1 49intergenic (‑2/+1)glpR/glpRpseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base G (15/32);  total (16/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGT  >  NC_000913_3_pae_tpiA/3560308‑3560594
                                                                                                                                                      |                                                                                                                                           
ccGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGCTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGcg                                                                                                                                             <  1:557055/149‑2 (MQ=255)
     atCGATAAACAGCGTCGAGCCATTGGGGATTTGCTTCGTCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGa                                                                                                                                        <  1:103097/149‑1 (MQ=255)
       cGATAAACAGCGTCGAGCCATTGGGGATTTGCTTCGCTACTGTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATc                                                                                                                                      <  1:809969/149‑1 (MQ=255)
       cGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATc                                                                                                                                      >  2:772062/1‑149 (MQ=255)
          tAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAgg                                                                                                                                   <  1:951222/149‑1 (MQ=255)
              cAGCGTCGAGCCATTGGGCATTTGCTCCGCCACTTTGCGTGCGATGCGCTCTTTTTCTTCGGTCAGGGTGGCCTTGCGATCGTGCCACGGCTTGTTAACCGAACTGTAAGGGAGCGCCGCACCGCAGTGAGT‑GGC‑AAGAATCAGGtttt                                                                                                                               >  2:162951/1‑149 (MQ=255)
               aGCGTCGTGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTTTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTg                                                                                                                              <  1:200205/149‑1 (MQ=255)
                   tCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCCCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGGGGCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTcc                                                                                                                          <  1:277958/149‑1 (MQ=255)
                     gtgcgaTTGGGGATTGGCTCGGCTACTTTGCGGCCGATGCGTTCTTTTTCTTGGGGCTGGGTGGCCTTGGGATCGGGCCACGGCGTGTTAACCGACCGGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTTCGc                                                                                                                        <  2:508744/144‑1 (MQ=255)
                       gCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACCGCGTGTTAACCGAAGTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCa                                                                                                                      >  2:789287/1‑149 (MQ=255)
                         cATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGc                                                                                                                    >  1:341851/1‑149 (MQ=255)
                              gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt                                                                                                               <  1:779074/149‑1 (MQ=255)
                                 aTTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                            <  1:948930/149‑1 (MQ=255)
                                      cTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgc                                                                                                       >  1:391760/1‑149 (MQ=255)
                                         ggCCACGTGGCGGGGTGTGCGCTCTTTTTGTTCGGTTTGGGTGGTCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc                                                                                                    <  2:827544/148‑1 (MQ=255)
                                         cGCCACTGTGCGGGCGATGCGCTCTTTTTCTGCGGTGTGGGTGGGATGGCGATCGGTCCACCGCGCATTTAACAAACACGTATGTTGTTCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc                                                                                                    <  2:521257/149‑1 (MQ=255)
                                                    gggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                                                         >  1:824593/1‑149 (MQ=255)
                                                           cccctcaTTTTCTGCCGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                                  <  2:200015/146‑1 (MQ=255)
                                                            cgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGTTTGTGTCACGGCGGGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGAc                                                                                 <  1:193942/149‑1 (MQ=255)
                                                                     tcgtgggTCGGGGTGGCCTTGGGTTCGGGCTCCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACGGCCATGA‑T‑GGCGCGGGTTCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGATCAGTCTGCGGGCTGACGGAGATATg                                                                        <  2:86320/144‑1 (MQ=255)
                                                                       ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTTAGGTCGCGGCGAATCGTCTGCGGGCTGACGGCGAAATgtt                                                                      >  2:607550/1‑147 (MQ=255)
                                                                          ggTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTa                                                                   <  2:763645/149‑1 (MQ=255)
                                                                            tCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAcc                                                                 >  2:407006/1‑149 (MQ=255)
                                                                                ggcggCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACAGCCATGA‑T‑GCCGCAGGCTCAGGTTTTGCTCCGCCAGCTCATTGAGGTAGCGACGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAccgact                                                             >  2:841120/4‑145 (MQ=255)
                                                                                  tGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCAATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGctct                                                           >  2:875668/1‑149 (MQ=255)
                                                                                     gcTTGCGATCGTGCCCCGGCGTGGTATCCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg                                                        <  2:678929/148‑1 (MQ=255)
                                                                                     ccTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCCGCTCATTGAGGTGGCGGCGAATAGTCTGCGGTCTGACGGAGAAATGTTCTACCAGCTCTTCg                                                        >  2:194560/1‑149 (MQ=255)
                                                                                     ccTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAGGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg                                                        <  1:331565/149‑1 (MQ=255)
                                                                                       ttGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCATCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGt                                                      <  1:330985/149‑1 (MQ=255)
                                                                                            catgttccACGGCTTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGa                                                 <  2:213162/143‑1 (MQ=255)
                                                                                            aTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGTGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGa                                                 <  1:378777/149‑1 (MQ=255)
                                                                                             tCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGGTTTGCTCCGCCAGCTCATTGAGTTCGCGTCGAATAATCTTCGGGCTGACAGAGACATCAACGACCACCGCTTAGGTACtaaa                                                >  1:281162/1‑146 (MQ=255)
                                                                                                     ccgcctgtTAACCCAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTCCGGGCTGACGGAGAAATGCTCTATCAGCTCTTCGGTCCTGACATAACCct                                        <  1:856136/144‑1 (MQ=255)
                                                                                                          tgtTAGCCGAACGTGAAGGCAGCGTCGCACCGCCATGA‑TGGGG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGCCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGt                                   <  2:7630/149‑1 (MQ=255)
                                                                                                           gtTCACCTAACTGGAAGCCAGCTCCGCACCGCCAGGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTCACGTAGAAATGCTCTACCATCTCTTCGGTACTCATATTACCCTGCTGtt                                  <  2:946944/149‑1 (MQ=255)
                                                                                                           gtTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGtt                                  <  2:391760/149‑1 (MQ=255)
                                                                                                                 cGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCa                            <  1:372625/149‑1 (MQ=255)
                                                                                                                      tGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTTTTTAACCAGTTCg                       >  2:809509/1‑149 (MQ=255)
                                                                                                                       ggAAGGCAGCGTAGCACGGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGGTCATTGAGGTCGCGGTGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGTTATTCGGTACTGACATAACCCTGCTGTTTAACCTGTTCGa                      <  2:734300/149‑1 (MQ=255)
                                                                                                                       ggAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGc                                                                                                                        >  1:785279/1‑51 (MQ=255)
                                                                                                                       ggAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGc                                                                                                                        <  2:785279/51‑1 (MQ=255)
                                                                                                                        gAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATTCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat                     <  2:341851/149‑1 (MQ=255)
                                                                                                                          aGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGataa                   <  1:178433/149‑1 (MQ=255)
                                                                                                                           ggCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGataat                  >  1:289624/1‑149 (MQ=255)
                                                                                                                            gCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGataata                 <  1:891479/149‑1 (MQ=255)
                                                                                                                              aGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATAcc               <  1:599635/149‑1 (MQ=255)
                                                                                                                                cgccgcACCGCCATGA‑T‑GGCGCAGGATCAGGTCTTGCTCCGCCAGCTCAGTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGt             <  2:51438/149‑1 (MQ=255)
                                                                                                                                          ccATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTAGATAATACCGTTGTGACGTtg   >  1:908696/1‑149 (MQ=255)
                                                                                                                                           tatga‑t‑gGCGCAGGATTAGGTTTTGCTCCGCCTGTTGATGGAGGGGGTTGTGAATGGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACTTAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTtgt  <  2:477625/148‑1 (MQ=255)
                                                                                                                                           cATGA‑G‑GGCGCAGGATCAGGGTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTtgt  <  2:979351/149‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                           
CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGT  >  NC_000913_3_pae_tpiA/3560308‑3560594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A