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
A14 F8 I1 R1 16 57.5 2022698 92.3% 1866950 143.6

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.G95.2% 122.9 / ‑1.2 42intergenic (‑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 . (0/2);  new base G (15/25);  total (15/27)
Fisher's exact test for biased strand distribution p-value = 5.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTG  >  NC_000913_3_pae_tpiA/3560314‑3560587
                                                                                                                                                |                                                                                                                                    
tCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCTATCGTGCCACGGCGCGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGAt                                                                                                                                <  1:891453/149‑1 (MQ=255)
  gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCa                                                                                                                              >  1:325727/1‑149 (MQ=255)
   aTAAACATCGTCGAGCCTTTGGGGATTT‑CCCCGCCCCTTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCAATAGGGCCACGGCGTGTTCACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAg                                                                                                                             <  1:651369/149‑1 (MQ=255)
   aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTAGGTGGCCTTGCGATCGTGCCACGACGTGTTAACCGAACTGGAAGGCAGCGCCGAACCGCCATAAT‑GGCGCAGGATCAg                                                                                                                             >  1:261911/1‑149 (MQ=255)
   aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCACTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAg                                                                                                                             <  1:593120/149‑1 (MQ=255)
    tAAACAGCGTCGGGGCATTGGGGAGTTGCTCCCCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAgg                                                                                                                            <  2:2617/149‑1 (MQ=255)
    tAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAgg                                                                                                                            <  1:707907/149‑1 (MQ=255)
     aaaCAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAgga                                                                                                                           >  1:294511/1‑148 (MQ=255)
      aaCAGGGACGAGCCATTGGTGATTTGCGACGCCAG‑TAGGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGAGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGtt                                                                                                                          <  2:506506/149‑1 (MQ=255)
        cAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCGCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTGAACCGAACTGGAAGGCAGCGCCCCACCGCCAAGAT‑GGCGCAGGAGCGAGtttt                                                                                                                        >  2:12014/1‑149 (MQ=255)
                        gggATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt                                                                                                        <  2:118612/149‑1 (MQ=255)
                        gggATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt                                                                                                        <  1:714244/149‑1 (MQ=255)
                        gggATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGATCAtt                                                                                                        >  1:200952/1‑149 (MQ=255)
                          gATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGa                                                                                                      <  1:230981/149‑1 (MQ=255)
                                  ccGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGTCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                              >  2:881076/1‑149 (MQ=255)
                                   cGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc                                                                                             <  1:505815/149‑1 (MQ=255)
                                        c‑TTTGCGGGCGTTGCGCCCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGACGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa                                                                                        <  1:147603/149‑1 (MQ=255)
                                        c‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa                                                                                        >  2:594654/1‑149 (MQ=255)
                                          tttGCGGGCGATGCGCTCTTTTTCTTCGGTATGGGTGGCCTTGCGATCGTGCAACGGGGTGTTAACCGAACTGGAAGGCAGCTCCGGACCACCATGAT‑GGCGCAGAAACAGGTTTTGCGTCGACAGCCAATCGCGGTAGCTGCGAACAg                                                                                       >  2:158286/1‑149 (MQ=255)
                                               gggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                                                  <  1:408451/149‑1 (MQ=255)
                                                 gCGACGCGCTCTGTTTCTTCGGTTTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCgg                                                                                <  1:854886/149‑1 (MQ=255)
                                                    aTGCGCTCTTTTTTTTTTTTTTTTGTGGCCTTGCGATCGTGCCACGGCTTGTTAACTGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTTTTCCTCCTTCTCATTGAGGTCGCGTCGTATAGTCTGCGGGCt                                                                             >  2:1001018/1‑149 (MQ=255)
                                                      gcgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                           <  1:594654/149‑1 (MQ=255)
                                                           ctTTTTCTTCGGTCTGGGTGGTCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgag                                                                      <  1:274418/149‑1 (MQ=255)
                                                                    cGGTCTGCGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctct                                                             <  2:334357/149‑1 (MQ=255)
                                                                      ggcggggTGGCCTGGCGGTCGTGCCGCGGTGGGTTGACTGAAGGGGGAGGCGGGGCCGCAGGGGCATGATGGGG‑CAGGATCAGGTGGTTTGCTGCCAGCGCAGGGAGGTCGCGGCGGATAGTCTGCGGGGTGACGGAGAAATGCTCTAc                                                           <  2:565140/145‑1 (MQ=255)
                                                                      gTCTGGGTGGCTGTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAc                                                           <  2:140180/149‑1 (MQ=255)
                                                                           ggTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCGCATTGAGGTCGCGGCGAATGGTCTGCGGGCTTACGGAGAAATGCTCTACCAGcc                                                      >  2:832754/1‑148 (MQ=255)
                                                                               gCCTTGAGATTGTGCCACGGCGGGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTc                                                  <  2:995873/149‑1 (MQ=255)
                                                                                     cGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGTCGACCTAGAAATGCTCTACCAGCTCTTCGGTACt                                            <  1:1001018/149‑1 (MQ=255)
                                                                                            gCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGGCATaa                                     >  1:37153/1‑149 (MQ=255)
                                                                                             ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCCACCAGCTCTTCGGTACTGACATAAc                                    >  2:449581/1‑149 (MQ=255)
                                                                                              cACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                                   >  1:386545/1‑149 (MQ=255)
                                                                                                   cGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct                              <  2:385660/149‑1 (MQ=255)
                                                                                                           ccGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATACTCTGCTGGCTGTCGGCGACGTCCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAAcc                      <  1:239327/149‑1 (MQ=255)
                                                                                                            cGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCa                     <  1:632602/149‑1 (MQ=255)
                                                                                                                  ggAAGGCAGCGCCGCACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCGGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                                   <  1:855408/129‑1 (MQ=255)
                                                                                                                  ggAAGGCAGCGCCGCACCGACATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                                   >  2:855408/1‑129 (MQ=255)
                                                                                                                   gAAGGCAGCGCGGCACCGCTATGGT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat              <  2:961578/149‑1 (MQ=255)
                                                                                                                       gCAGCGCCGCACCGGCATGATGGGA‑GAGGATCATGTTTTGCGCCGCCAGCTCATTGGGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGataata          <  2:202344/149‑1 (MQ=255)
                                                                                                                            gccgcACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGtt     <  1:881076/149‑1 (MQ=255)
                                                                                                                               gcACCGCCATGAT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTtgtg  >  2:1002531/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                    
TCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCAC‑TTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGAT‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTG  >  NC_000913_3_pae_tpiA/3560314‑3560587

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