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
A23 F6 I1 R1 16 59.9 2107472 93.9% 1978916 143.0

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.G97.7% 133.4 / ‑2.9 44intergenic (‑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 . (1/0);  new base G (25/18);  total (26/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTT  >  NC_000913_3_pae_tpiA/3560308‑3560597
                                                                                                                                                     |                                                                                                                                               
ccGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGTCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATAGcg                                                                                                                                                 >  1:832282/1‑148 (MQ=255)
       cGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATc                                                                                                                                         >  1:636394/1‑149 (MQ=255)
        gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACGGCCATGATGGCGCA‑GGATCa                                                                                                                                        >  1:573444/1‑149 (MQ=255)
         aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAg                                                                                                                                       >  1:126287/1‑149 (MQ=255)
         aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAg                                                                                                                                       <  2:975298/149‑1 (MQ=255)
            agcAGCGGCGAGCAATTGGGGATTCGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGCCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑GTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGtt                                                                                                                                    <  2:746704/147‑1 (MQ=255)
             aCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGTTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAGCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGttt                                                                                                                                   >  2:510672/1‑149 (MQ=255)
               aGCGTCGAGCCATTGGGGATTTGCTCCGCCACGTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTg                                                                                                                                 <  2:72315/149‑1 (MQ=255)
                   gggggCCATGGGGGATTTGCTCCGCCACTTGGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCCCGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTcc                                                                                                                             <  2:811768/145‑1 (MQ=255)
                     gAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTGTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGGACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGc                                                                                                                           >  2:797746/1‑149 (MQ=255)
                     gAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGc                                                                                                                           <  1:365649/149‑1 (MQ=255)
                       gCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCa                                                                                                                         >  1:538590/1‑149 (MQ=255)
                         cATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGTGCTTGCGATCGTGCCCCGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGc                                                                                                                       >  2:119328/1‑149 (MQ=255)
                            tGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCa                                                                                                                    >  1:313138/1‑149 (MQ=255)
                                 aTTTGCTCCGCCACTTTTCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                               <  1:596412/149‑1 (MQ=255)
                                  tttGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAgg                                                                                                              >  1:857933/1‑149 (MQ=255)
                                  taagCTCCGCCACATTGCGGGCGATGCGCTCTTTTTCTTCAGTCTGGGTGGCCGTACGATCGTGCGACGGCGGG‑TCGACCGAAAGGGAAAACAGCGCCACACCGCCATGAGGGCGCA‑GGATCACGCTAAGCTCCGCCAGCGCATCGacg                                                                                                              >  2:320299/4‑147 (MQ=255)
                                      cTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgc                                                                                                          >  1:272981/1‑149 (MQ=255)
                                        ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGTTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                        <  2:826812/149‑1 (MQ=255)
                                        ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                        <  1:796740/149‑1 (MQ=255)
                                         cGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCAACGGCCTGTTTCAACG‑ACTTTGTTGCAGCTCCTCACCGCCAAGATCGCGAA‑GGATCAGGTTTTGCCCCGCCCGCTCATTGAGGGCtcggc                                                                                                       >  2:143/1‑149 (MQ=255)
                                               tttGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGCGGTCGCCGAGAATAg                                                                                                 >  2:990456/1‑149 (MQ=255)
                                               tttGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAg                                                                                                 >  1:945255/1‑149 (MQ=255)
                                                       cGATGCGTTGTTTTTCTGCGGTGTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCggg                                                                                         <  2:150910/149‑1 (MQ=255)
                                                         gtGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATGGTCTGCGGGCt                                                                                       <  1:659695/148‑1 (MQ=255)
                                                           gcgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                                     <  1:411016/149‑1 (MQ=255)
                                                                   tttCTTCGGTCTGGTGGGCCTGGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                                             <  2:163781/149‑1 (MQ=255)
                                                                       ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATgat                                                                         >  1:85112/1‑147 (MQ=255)
                                                                           gTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctctcc                                                                     >  1:1045395/1‑147 (MQ=255)
                                                                            tCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAAATGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTagc                                                                    >  1:274731/1‑147 (MQ=255)
                                                                                    gCCTTGCGATCGTGCCCCGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTc                                                            >  1:917703/1‑149 (MQ=255)
                                                                                      ctgggcgtCGTGCCACGGCGTG‑TTAACCGTACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCCCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGTGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                                          <  2:160858/142‑1 (MQ=255)
                                                                                      cTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                                          >  1:669257/1‑149 (MQ=255)
                                                                                      cTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACCGAGAAATCCACTCCCCGCTCTTCgg                                                          >  2:192618/1‑149 (MQ=255)
                                                                                                  ccACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGCTCAGGTCTTGCTCCGCCAGCTCCTTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGCGAAATGCTCTACCAACTCCTCGATCCTCGCATAAc                                              >  2:957561/1‑149 (MQ=255)
                                                                                                        cGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct                                        <  1:439024/149‑1 (MQ=255)
                                                                                                                aCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACTTAACAGTGCTGTTTAAc                                 >  2:1003091/1‑149 (MQ=255)
                                                                                                                  cGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCa                               <  2:669257/149‑1 (MQ=255)
                                                                                                                  cGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCa                               <  1:915353/149‑1 (MQ=255)
                                                                                                                     aCTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt                            <  1:119328/149‑1 (MQ=255)
                                                                                                                        ggAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                         <  2:284557/149‑1 (MQ=255)
                                                                                                                                gcgcCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACAAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCg                 >  2:73695/1‑149 (MQ=255)
                                                                                                                                  gccgcACCGCCATGATGGC‑GACGAAGCAAGTTTTGCTCCGCCAGCTCATGGAGGTCGCGGCGAATAGGCTGCGGGCTAACGGAGAAATGCCCTACCAGATCTTCGGTACTGGCATAACCCTGCTGTTTAACCACTTCGATAATAACGtc               >  2:514963/1‑148 (MQ=255)
                                                                                                                                           ccATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTtg      >  1:226313/1‑149 (MQ=255)
                                                                                                                                               gatgGCGCA‑GGAATAGGTTTTGCTCCGCCAGCTCGTTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGCAATGCTCTACCAGCTCTTCGGTACTTTCATAACCCTGCACTTTAACCACTTCGATAATACCCTTGTTACGTTGtgtt  >  2:164173/1‑149 (MQ=255)
                                                                                                                                                     |                                                                                                                                               
CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTT  >  NC_000913_3_pae_tpiA/3560308‑3560597

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