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
A6 F73 I1 R1 31 34.8 1203930 99.1% 1193094 139.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,560,4551.G97.8% 155.2 / ‑2.9 46pseudogene (151/758 nt)glpRDNA‑binding transcriptional repressor GlpR
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base G (19/26);  total (19/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

AAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTT  >  NC_000913/3560319‑3560584
                                                                                                                                          |                                                                                                                                 
aaaCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGcgca                                                                                                                                 <  2:315329/140‑4 (MQ=255)
   cggCGTGGAGCCTTGGGGGTTTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGGGTGTTAACCGAACGGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGa                                                                                                                              <  2:435400/138‑1 (MQ=255)
   cAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGa                                                                                                                              <  2:585864/140‑1 (MQ=255)
      cGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCa                                                                                                                           >  1:20063/1‑140 (MQ=255)
      cGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCa                                                                                                                           >  2:357110/1‑140 (MQ=255)
      cGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCa                                                                                                                           >  1:318070/1‑140 (MQ=255)
      cGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCa                                                                                                                           >  2:107204/1‑140 (MQ=255)
           aGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGttt                                                                                                                      >  2:535958/1‑140 (MQ=255)
                      ttttGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAg                                                                                                           <  2:62558/139‑1 (MQ=255)
                      ttttGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAg                                                                                                           <  2:319433/139‑1 (MQ=255)
                      ttttCCTCCTCCACTTTGTGGCCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTTTAAACCGAACTGGAAGGCGGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAg                                                                                                           <  2:447444/139‑1 (MQ=255)
                      aTTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAg                                                                                                           <  1:178166/140‑1 (MQ=255)
                               gCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                  >  2:331388/1‑140 (MQ=255)
                                             gATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGGGTTAACCGAACTGGCAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGCCGCGGCGAATAg                                                                                    >  1:256821/1‑140 (MQ=255)
                                              aTGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCGATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGt                                                                                   >  1:599261/1‑140 (MQ=255)
                                                gcgcTCTTTTTCTTCGGTCTGGGTGGCCTT‑CGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTg                                                                                >  1:526476/1‑140 (MQ=255)
                                                      tttttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGc                                                                           <  1:32711/140‑1 (MQ=255)
                                                         ttcttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                        >  1:442147/1‑140 (MQ=255)
                                                            ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                        <  2:559273/137‑1 (MQ=255)
                                                            ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                        >  1:559273/1‑137 (MQ=255)
                                                               ggTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgaga                                                                  <  1:286744/140‑1 (MQ=255)
                                                               ggTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgaga                                                                  <  1:395127/140‑1 (MQ=255)
                                                                    gggTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGc                                                             <  1:107204/140‑1 (MQ=255)
                                                                        ggCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGTAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTa                                                         >  1:550934/1‑140 (MQ=255)
                                                                          ccTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAcc                                                       >  2:300630/1‑140 (MQ=255)
                                                                            ttGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAg                                                     <  1:535958/140‑1 (MQ=255)
                                                                                 aTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt                                                <  2:499239/140‑1 (MQ=255)
                                                                                 aTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt                                                <  1:279117/140‑1 (MQ=255)
                                                                                    gTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                             >  2:588155/1‑140 (MQ=255)
                                                                                    gTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                             >  2:463676/1‑140 (MQ=255)
                                                                                      gCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTa                                           <  2:418865/140‑1 (MQ=255)
                                                                                       ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTAc                                          <  1:588155/140‑1 (MQ=255)
                                                                                               tgtTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa                                  >  1:350541/1‑140 (MQ=255)
                                                                                               tgtTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa                                  >  1:436272/1‑140 (MQ=255)
                                                                                                   aaCCGAACTGGAAGGTAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCct                              <  2:550934/140‑1 (MQ=255)
                                                                                                   aaCCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCct                              <  2:442147/140‑1 (MQ=255)
                                                                                                   aaCCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCct                              <  2:411512/140‑1 (MQ=255)
                                                                                                   aaCCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCct                              <  1:504068/140‑1 (MQ=255)
                                                                                                    aCCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa                                  <  2:498500/135‑1 (MQ=255)
                                                                                                    aCCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa                                  >  1:498500/1‑135 (MQ=255)
                                                                                                         aCTGGAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGtt                        >  1:480959/1‑140 (MQ=255)
                                                                                                             gaaggaagCGCAGCACCGCCATGACTGCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAAc                    <  2:599261/140‑1 (MQ=255)
                                                                                                             gAAGGCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAAc                    <  2:318070/140‑1 (MQ=255)
                                                                                                                ggCAGCGCCGCACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAg                 <  2:350541/140‑1 (MQ=255)
                                                                                                                     cgccgcACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa            <  2:566161/140‑1 (MQ=255)
                                                                                                                      gccgcACCGCCATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat           <  2:526476/140‑1 (MQ=255)
                                                                                                                               ccATGA‑TGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGtt  <  2:541328/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                 
AAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑TGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTT  >  NC_000913/3560319‑3560584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A