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
A24 F26 I1 R1 10 55.9 2015792 89.8% 1810181 144.1

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% 123.0 / ‑4.1 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 (18/23);  total (18/24)
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

ATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTT  >  NC_000913_3_bme_pgi/3560311‑3560584
                                                                                                                                                   |                                                                                                                                 
atatCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑cgcag                                                                                                                                >  2:896290/1‑145 (MQ=255)
   tCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGAt                                                                                                                             >  1:519470/1‑149 (MQ=255)
   tCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGAGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGAt                                                                                                                             >  2:215511/1‑149 (MQ=255)
    cGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATc                                                                                                                            <  1:670071/149‑1 (MQ=255)
          aCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGttt                                                                                                                      >  1:94020/1‑149 (MQ=255)
                        ttGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCATGCCACGGCGTGTTA‑ACCGAACTGGAAAGCAGCGCCGCACCGCCATGATTG‑CGCACGATCAAGTTTTGCTCCGCCAGCTc                                                                                                        >  1:780734/1‑149 (MQ=255)
                          ggggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCAt                                                                                                      <  1:164663/149‑1 (MQ=255)
                           gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt                                                                                                     <  2:184714/149‑1 (MQ=255)
                            ggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTg                                                                                                    <  2:702290/149‑1 (MQ=255)
                             gATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGa                                                                                                   >  1:774744/1‑149 (MQ=255)
                                    tCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCCCGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATAAAGG‑CGCAGGATAAGGGTTTGCTCCGCCGTCTCAATGAGGTcacg                                                                                            >  2:299254/1‑149 (MQ=255)
                                    tCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgcg                                                                                            >  2:919426/1‑149 (MQ=255)
                                       gCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                  <  1:949288/140‑1 (MQ=255)
                                       gCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTCAg                                                                                                  >  2:949288/1‑140 (MQ=255)
                                        ccACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCCCCCCCAGCACATTGAGGTCGCGGCGa                                                                                        >  2:440906/1‑149 (MQ=255)
                                              tGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGGCGCGGCGAATAGTc                                                                                  <  2:653474/149‑1 (MQ=255)
                                                      aTGCGCTCTTTTTCTGCGGTCTGGGTGGCCGTGCTGTCGTTCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGACCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCt                                                                          <  1:890301/149‑1 (MQ=255)
                                                         cgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTACAAGGTACT‑TTCTGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGAc                                                                       <  1:987853/149‑1 (MQ=255)
                                                           ctctTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGCAGAGGGGAATAGTCTGCGGGCTGACgg                                                                     >  1:936104/1‑149 (MQ=255)
                                                                tttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGAt                                                                                                                             <  2:461059/88‑1 (MQ=255)
                                                                tttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGAt                                                                                                                             >  1:461059/1‑88 (MQ=255)
                                                                    gtcGGGCAGGGTGGCCTTGCGATGGGGCCACGGCGGGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct                                                            <  2:84510/148‑1 (MQ=255)
                                                                          gtgcgTGGACTTGCTATCGTGCCACGGCGTGTCA‑ACCGAACTGGATGGCAGCGCCGCACCTCCATGATGG‑CGCAGCATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGCCTGCGGGCTGACGGAGAAATGCTCTACCa                                                      <  2:73323/145‑1 (MQ=255)
                                                                               tGGCCTTGCGATGCTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGctct                                                 <  1:327014/149‑1 (MQ=255)
                                                                                  ccTTGCGATCGTGCCACGGCATGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg                                              >  1:1000144/1‑149 (MQ=255)
                                                                                     tGCGATCGTTCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCCCCGCTAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTa                                           <  1:514505/149‑1 (MQ=255)
                                                                                        gATAGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCAGCGGGCTGACGGAGAAATCCCCTACCAGCTCTTCGGTACTg                                        >  2:266883/1‑149 (MQ=255)
                                                                                                cACGGCGTGTTA‑ACCGAACTGGACGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                                <  1:486431/149‑1 (MQ=255)
                                                                                                 aCGGCGTGTTA‑ACCGAGCTGGAAGGCAGCGCCGCACCGTCATGATGGTG‑CATGATCAGGTTTTTCTCCGTCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAccc                               <  1:266883/149‑1 (MQ=255)
                                                                                                     cGTGTTA‑ACCGAACGTGAAGGCGGCGCCGCACCGCCATGATGG‑CGCAGGACCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct                           <  2:70461/149‑1 (MQ=255)
                                                                                                      gtgtTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgctg                          >  1:18354/1‑149 (MQ=255)
                                                                                                       tgtTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGt                         <  1:947573/149‑1 (MQ=255)
                                                                                                        gtTA‑ACCGAATTGGAAGGAAGCGGCGCACCGCCATGATGG‑CGCATGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGGCTGCGGTCTGACGGAGAAATGCTCTATCAGCTCTTCGGTACTGACATAACCCTGCTGtt                        <  1:333413/149‑1 (MQ=255)
                                                                                                             aCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGCACAGACATAACCCTGCTGTTTAAc                    <  2:94020/149‑1 (MQ=255)
                                                                                                                  cgtGGAAGGCAGGGACGCACGGCAATGCGGG‑CGCAGGATCAGGTTTTGCTCGGCCAGCGGATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCGCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt               <  2:479901/147‑1 (MQ=255)
                                                                                                                      gAAGGCCGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat           <  1:111354/149‑1 (MQ=255)
                                                                                                                      gAAGGCAGCGCCGCACCGCGATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCACGGCGAATAGTCTGCGGGCTGACGGAGACATGCTCTATCAGCCCTTCGGTACTGACATAACCCTTCTGTTTAACCAGTTCGat           >  2:849995/1‑149 (MQ=255)
                                                                                                                      gAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat           >  2:811753/1‑149 (MQ=255)
                                                                                                                      gAAGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat           <  1:520822/149‑1 (MQ=255)
                                                                                                                        aGGCAGCGCCGCACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCCCCAGCTCATTGAGGCCGCGGCGAATAGTCTGCGGTCTGACGGAGAAATGATCTACCAGCTCTTCGGTACTGTCATACCCCTGCTGTTTAACCAGCTCGatga         >  2:488363/1‑147 (MQ=255)
                                                                                                                               gccgcACCGCCATGATGG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGtt  <  1:419562/149‑1 (MQ=255)
                                                                                                                                           tgatgG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctc                                                           >  2:583956/1‑80 (MQ=255)
                                                                                                                                           tgatgG‑CGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctc                                                           <  1:583956/80‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                 
ATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTA‑ACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGG‑C‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTT  >  NC_000913_3_bme_pgi/3560311‑3560584

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