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
A13 F6 I2 R1 16 27.9 994488 92.8% 922884 143.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 4,110,747 G→T intergenic (+62/+784) cdh → / ← yiiQ CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA4,110,7470GT95.1% 117.8 / NA 41intergenic (+62/+784)cdh/yiiQCDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base T (24/15);  total (25/16)
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

CTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCAGT  >  NC_000913_3_pae_tpiA/4110602‑4110892
                                                                                                                                                  |                                                                                                                                                 
cTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGcc                                                                                                                                                >  1:480323/1‑149 (MQ=255)
 tGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTCAGGCAAAGAGTTAAGGAAAGTAAGTGCCGGATCTGAACTCCGGCACCTGTCAG‑ACTTAAGGCTGccc                                                                                                                                               >  1:175940/1‑149 (MQ=255)
      acacAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCccgccg                                                                                                                                          >  1:211491/1‑149 (MQ=255)
          aaCGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑CCTTAAGGCTGCCCCCCCGCGAg                                                                                                                                      >  2:370087/1‑149 (MQ=255)
           aCGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCGGGGAGc                                                                                                                                     >  1:98140/1‑149 (MQ=255)
                aTCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGttt                                                                                                                                >  1:119299/1‑149 (MQ=255)
                   tACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTGTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGc                                                                                                                             >  1:267430/1‑149 (MQ=255)
                      tGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGATAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAAGCGGACTTTCCTCGAGCGGTTTGGCCaa                                                                                                                          >  2:374998/1‑149 (MQ=255)
                             tAACCGTGCTTCGGAGGAGGAAATTCATGATCAGCAGTGTGAGCTTTTGCGTTAAGGCGAAGACTTAAGGAAAGTACGTGCGGAATATGAAACCCGGTAGCTGTCAG‑ACTTAAGGCTGCGCCGCCGCGAGCGGTTTCGCCAATTCTAAg                                                                                                                   <  2:450576/149‑1 (MQ=255)
                              aaCCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGACTTCTTGATCCGGCACCT‑TCAGCACGTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGa                                                                                                                  <  1:367686/149‑1 (MQ=255)
                                 cGTGCTTCAGCCGAGGCAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCt                                                                                                               >  2:343811/1‑149 (MQ=255)
                                      ttCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGa                                                                                                          <  1:103094/149‑1 (MQ=255)
                                      ttCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCAGGCACCTGTAAG‑ACTTAAGGCTCGCCCGCCCCCAGCGGTTTCGCCAATTCTCAGATCTTAAgc                                                                                                          >  2:91875/1‑148 (MQ=255)
                                         aGCCGAGGAAATTCAGGATCATCAGTCAGCACGTCCCCTTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGatat                                                                                                       >  1:492190/1‑149 (MQ=255)
                                                    ttCAGGATCATCGGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGc                                                                                            >  1:84020/1‑149 (MQ=255)
                                                    ttCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGc                                                                                            <  1:477440/149‑1 (MQ=255)
                                                     tCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAg                                                                                                           >  1:29983/1‑133 (MQ=255)
                                                     tCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAg                                                                                                           <  2:29983/133‑1 (MQ=255)
                                                         gATCATCGGTGTGAGATTTTGAGTTCGGGCGGAGGGTTGAGAACAGTAACGGCCGGATTTGTAATTCTGCACCAGTCAT‑ACTTAAGGCTGCCCCGGCGCGAGCGTTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCa                                                                                       <  2:118353/149‑1 (MQ=255)
                                                             agcaGCGTGAGATTTTGCGTTAAGGCGAAGAGCTAAGGAAAGTAAGTCCCGGCTCTGAAATCCGCCCCCTGTCAG‑ACCTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCCATTCTAAACTCTCAAGCTACCGGCCTTTTGCCTTccctcc                                                                                   >  2:341283/3‑144 (MQ=255)
                                                              tcggtgtGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCt                                                                                  <  2:84020/146‑1 (MQ=255)
                                                               caGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTg                                                                                 <  1:282377/149‑1 (MQ=255)
                                                                      ggaTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGc                                                                          <  2:229007/148‑1 (MQ=255)
                                                                      ggaTTGTGCGTTAAGGCGAAGGTTTAAGGAAAGTAAGTGCCGTATATGAAATCCGGCACCTGTCAG‑AATTAGGGCGGCCCCGTCGCGTGCCGTTTCGCTAATTCTAAGATCTCAAGATTTGGGTCTTTTGCCTTCACGGCTGCGCTTGc                                                                          <  2:2187/148‑1 (MQ=255)
                                                                         ttttGGGTTAAGGGGAAGAGTTAGGGAAAGTGAGTGCCGGATATGGAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAg                                                                       <  2:59397/149‑1 (MQ=255)
                                                                                 tAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTc                                                               >  1:1337/1‑149 (MQ=255)
                                                                                        aaGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGt                                                        >  2:363391/1‑149 (MQ=255)
                                                                                        aaGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGt                                                        <  2:409626/149‑1 (MQ=255)
                                                                                             ttAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCGGCAACACTCCCCTCGTGCCGa                                                   >  2:229480/1‑149 (MQ=255)
                                                                                             taaaGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGa                                                   <  1:136807/147‑1 (MQ=255)
                                                                                                aGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACACCCCTCGTGCCGGGtt                                                >  1:65342/1‑149 (MQ=255)
                                                                                                  gAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTa                                              >  2:343391/1‑149 (MQ=255)
                                                                                                          gtGCCGGATATGAAATCCGGCACCTGTCCG‑CCTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGAACTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGcgccgc                                      >  2:234855/1‑149 (MQ=255)
                                                                                                          gtGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGc                                      <  1:456722/149‑1 (MQ=255)
                                                                                                                gATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAAc                                >  2:11824/1‑149 (MQ=255)
                                                                                                                        aTCCGGCACCTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCtctc                        >  1:249986/1‑149 (MQ=255)
                                                                                                                                ccTGTCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCa                <  1:4986/149‑1 (MQ=255)
                                                                                                                                    tCAG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAc            >  1:182659/1‑149 (MQ=255)
                                                                                                                                      aG‑ACTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACCCTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAccc          >  2:178741/1‑149 (MQ=255)
                                                                                                                                          cTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATgg                                                                                                     <  2:396438/55‑1 (MQ=255)
                                                                                                                                          cTTAAGGCTGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATgg                                                                                                     >  1:396438/1‑55 (MQ=255)
                                                                                                                                               ggctgcCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCAGt  >  2:41717/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                 
CTGGCGACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAG‑ACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCAGT  >  NC_000913_3_pae_tpiA/4110602‑4110892

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A