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
A20 F7 I1 R1 11 43.1 1491906 94.3% 1406867 142.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_bme_pgi 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_bme_pgi3,560,4551.G97.6% 140.3 / ‑3.9 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 . (0/1);  new base G (24/17);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTG  >  NC_000913_3_bme_pgi/3560309‑3560593
                                                                                                                                                   |                                                                                                                                           
cGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAAGCGTACTGTAAGGCAGCGCCGCAGCGCCATGATGGcgc                                                                                                                                            <  2:720006/149‑3 (MQ=255)
       gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCa                                                                                                                                    >  1:449496/1‑149 (MQ=255)
        aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAg                                                                                                                                   >  2:210865/1‑149 (MQ=255)
         tAAACAGGGTCGGGCCTTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTGTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAgg                                                                                                                                  <  2:704195/149‑1 (MQ=255)
           aaCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATTGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGtt                                                                                                                                >  2:347573/1‑149 (MQ=255)
                 gTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTc                                                                                                                          <  2:677468/149‑1 (MQ=255)
                    gAGCCATTGGGGATTTGCCCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGc                                                                                                                       <  1:469567/149‑1 (MQ=255)
                       ccATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCTGCCAg                                                                                                                    >  1:547045/1‑149 (MQ=255)
                         aTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCt                                                                                                                  >  1:99520/1‑149 (MQ=255)
                         aTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGACGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCt                                                                                                                  >  1:513969/1‑149 (MQ=255)
                         aTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTGTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCt                                                                                                                  <  1:127397/149‑1 (MQ=255)
                                      tCCGCCACTTTGCGGGCGAAGAACACTCCCTATCCGATATCGGCAGCCTTGCAATCGTTACACGGCGTTTTAACCGAACTCACAGGCAGCGCAGCACCGCCCTGATGGCGCA‑AGATCCGGTTTCGCTCCGCCAGCTCCTTGCGGTcgcg                                                                                                     >  2:149108/1‑149 (MQ=255)
                                        cGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc                                                                                                   >  2:94916/1‑149 (MQ=255)
                                         gCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggcg                                                                                                  >  1:637066/1‑149 (MQ=255)
                                           cACTTTGCGGGCGGTGCGCTATTTCTCTTCGTGGTGGTTGGCCTTGCGATATTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCACGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGaa                                                                                                <  1:475163/149‑1 (MQ=255)
                                                tGCGGGCGATGCGCTCTTTTTCTTCGGTCGGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTc                                                                                           <  1:478169/149‑1 (MQ=255)
                                                   gggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGc                                                                                        >  1:665237/1‑149 (MQ=255)
                                                    ggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCCATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCg                                                                                       <  1:697426/149‑1 (MQ=255)
                                                       gATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGc                                                                                    >  1:63549/1‑149 (MQ=255)
                                                                     cttcGGTCTGGGTGGCATTACGGTCGTGCCACGGCGTGTGAACAGAACTGGAGGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCCGACGGAGAACTGc                                                                      >  2:68876/1‑149 (MQ=255)
                                                                      ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct                                                                     >  1:297845/1‑149 (MQ=255)
                                                                        cGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctct                                                                   <  2:449496/149‑1 (MQ=255)
                                                                            cTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCa                                                               <  2:63549/149‑1 (MQ=255)
                                                                                gTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCATCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGCCGGAGAAATGCTCTACCAGcta                                                           >  2:742845/1‑148 (MQ=255)
                                                                                 tGGCCTTGCGATCGTGCCACGGCGTATTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGctct                                                          >  1:676621/1‑149 (MQ=255)
                                                                                          gATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTg                                                 >  2:485477/1‑149 (MQ=255)
                                                                                          gATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTg                                                 >  2:486052/1‑149 (MQ=255)
                                                                                             cGTGCCACGGCGTGTTCACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑GATACCGCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACa                                              <  1:548749/149‑1 (MQ=255)
                                                                                                   aCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGc                                                                      <  1:636392/119‑1 (MQ=255)
                                                                                                   aCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGc                                                                      >  2:636392/1‑119 (MQ=255)
                                                                                                     ggCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctg                                      <  1:347573/149‑1 (MQ=255)
                                                                                                      gCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgc                                     >  2:34520/1‑149 (MQ=255)
                                                                                                              aCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTCCCACCTCTTCGGTACTGACATAACCCTGCTGTTTAAc                             <  1:210865/149‑1 (MQ=255)
                                                                                                               ccGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAAcc                            >  2:422856/1‑149 (MQ=255)
                                                                                                                   aCTGGAAGGCAGCGCCGCAGCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt                        <  2:525052/149‑1 (MQ=255)
                                                                                                                   aCTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt                        <  1:79175/149‑1 (MQ=255)
                                                                                                                     tGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCg                      >  1:636952/1‑149 (MQ=255)
                                                                                                                      ggAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                     <  1:34520/149‑1 (MQ=255)
                                                                                                                       gAAGTCATCGCCGCGCCGCCAGGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAGTAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat                    >  2:289477/1‑149 (MQ=255)
                                                                                                                           gCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGCGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGacgata                >  2:639904/1‑144 (MQ=255)
                                                                                                                                gccgcACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCTGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGtt           <  2:547045/149‑1 (MQ=255)
                                                                                                                                  cgcACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTtgt         <  1:422856/149‑1 (MQ=255)
                                                                                                                                         ccATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTtg  >  1:650976/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                           
CGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTG  >  NC_000913_3_bme_pgi/3560309‑3560593

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A