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
A21 F73 I1 R1 19 39.3 1399748 93.9% 1314363 140.8

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.G93.2% 130.0 / 2.1 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 . (1/2);  new base G (18/23);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGC‑‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGAT  >  NC_000913_3_pae_tpiA/3560307‑3560575
                                                                                                                                                      |                                                                                                                         
gCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGc                                                                                                                            >  1:635235/1‑149 (MQ=255)
      atCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGa                                                                                                                     >  1:358758/1‑149 (MQ=255)
         gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCCCCGCCCCGCCATGAT‑GGCG‑CAGGATCa                                                                                                                  >  1:141668/1‑149 (MQ=255)
           tacaCAGCGTCGTGCCATTGGGGATGTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAgg                                                                                                                <  1:43576/146‑1 (MQ=255)
              aCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGAGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGGG‑‑CAGGATAAGGttt                                                                                                             >  2:13141/1‑149 (MQ=255)
                gcggccGAGCCATTGGGGATTGGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGGGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTg                                                                                                           <  2:358758/144‑1 (MQ=255)
                 gCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGc                                                                                                          <  1:450070/149‑1 (MQ=255)
                   gTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTc                                                                                                        <  1:445164/149‑1 (MQ=255)
                      gAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGGTGCGGTTTTGCTCCGc                                                                                                     >  1:226675/1‑149 (MQ=255)
                          cATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCCGGGCGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGc                                                                                                 <  1:161883/149‑1 (MQ=255)
                             tGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCa                                                                                              <  1:252146/149‑1 (MQ=255)
                               gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGttt                                                                                                             <  2:78973/132‑1 (MQ=255)
                               gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGttt                                                                                                             >  1:78973/1‑132 (MQ=255)
                               gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCAtt                                                                                            <  1:119501/149‑1 (MQ=255)
                                          cGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc                                                                                 >  1:497793/1‑149 (MQ=255)
                                               cTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa                                                                            <  2:202040/149‑1 (MQ=255)
                                                  tGCGGGCGATGCGCTCTTTTTCTTCGGTCTCGGTGGCCTTGCGATCGTGCGACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTc                                                                         <  1:654510/149‑1 (MQ=255)
                                                     gggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGCATAGTCTGc                                                                      >  2:370988/1‑149 (MQ=255)
                                                     gggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCAGCACCGGCATTAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                                      <  1:310101/149‑1 (MQ=255)
                                                      ggggaggcgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCg                                                                     <  2:125782/143‑1 (MQ=255)
                                                       gCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCgg                                                                    <  2:525747/149‑1 (MQ=255)
                                                       gCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCACGCT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCCGCTCATTGAGGTCGCGGCGAATAGTCTGCgg                                                                    <  2:519482/149‑1 (MQ=255)
                                                        cGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCGCCGCCAGCTCATTGAGTTCGCGGCGAATAGTCTGCggg                                                                   <  2:615495/149‑1 (MQ=255)
                                                         gatgatctctTTTTCTTCGGTCTAGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACCGGAAGGCAGCGCCGCGCCGCCATGATGGGT‑‑CTGGATCAGGTGTTGCTTCGCCAGCTTATTGAGGTCGCGGCGAATAGTCTGCGGGc                                                                  <  1:591365/143‑1 (MQ=255)
                                                            gcgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGttt                                                                                                             <  2:320961/103‑1 (MQ=255)
                                                            gcgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGttt                                                                                                             >  1:320961/1‑103 (MQ=255)
                                                                    tttCTTCGGGCTGGTTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                       <  2:425569/149‑1 (MQ=255)
                                                                     ttcttcGGTCTGGGTGGCCTTGCGATCGAGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAAt                                                      <  2:114175/149‑1 (MQ=255)
                                                                        ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGCAATGct                                                   >  1:4744/1‑149 (MQ=255)
                                                                                   tGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGga                                                           >  1:303643/1‑130 (MQ=255)
                                                                                   tGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGga                                                           <  2:303643/130‑1 (MQ=255)
                                                                                      ccTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg                                     <  1:446447/149‑1 (MQ=255)
                                                                                       cTTGCGATCGTTCCACAGCGTGTTAACCGGACTGGAAGGCAGCGCAGCATCGCCATGAT‑GGCG‑CAGGATCAGGTTTGGCTCCACCGGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAGTCGCCTACGGGCTCTTCgg                                    >  2:632939/1‑149 (MQ=255)
                                                                                       cTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGATTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgc                                    >  1:438336/1‑148 (MQ=255)
                                                                                        ttGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt                                       <  1:169088/145‑1 (MQ=255)
                                                                                        ttGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt                                       >  2:169088/1‑145 (MQ=255)
                                                                                        ttGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATAAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCGCTACCAGCTCTTCGGt                                   >  1:378499/1‑149 (MQ=255)
                                                                                                 ggCCAAGGCGTGTGACCCGAACGTGAAGGCAGCGCGGCACCGCCATGAT‑GGCGGCAGCA‑CACGTATTGCTTCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATa                          <  1:163181/148‑1 (MQ=255)
                                                                                                    cACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                       >  1:241874/1‑149 (MQ=255)
                                                                                                     aCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCCCGGCGAAGAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAccc                      >  1:233786/1‑149 (MQ=255)
                                                                                                                 gcGAACGGGAAGGCATCGCCGCACCGCCATGGTGGGC‑‑GAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAAcc          <  2:564762/148‑1 (MQ=255)
                                                                                                                   gcaCTGGAAGGCAGCGCCGCACCGCCAAGAT‑GGCG‑CAGGATCAGGTTTTGCTCCTCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAg        <  1:224642/147‑1 (MQ=255)
                                                                                                                    aaCTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTGTTCGGTACTGACATGAGCCTGCTGTTTAACCAGt       >  1:578821/1‑149 (MQ=255)
                                                                                                                    aaCTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGt       >  2:82064/1‑149 (MQ=255)
                                                                                                                         gAAGGCAGCGCCGCACCGCCATGAT‑GGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat  >  2:531704/1‑149 (MQ=255)
                                                                                                                                                      |                                                                                                                         
GCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGC‑‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGAT  >  NC_000913_3_pae_tpiA/3560307‑3560575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A