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
A22 F27 I1 R1 17 36.9 1290494 93.0% 1200159 143.6

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_tpiA4,110,7470GT93.0% 115.4 / ‑1.2 43intergenic (+62/+784)cdh/yiiQCDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (1/2);  new base T (24/16);  total (25/18)
Fisher's exact test for biased strand distribution p-value = 5.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCC  >  NC_000913_3_pae_tpiA/4110610‑4110888
                                                                                                                                         |                                                                                                                                              
acaACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGGAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCcgcg                                                                                                                                     >  2:413809/1‑149 (MQ=255)
acaACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCcgcg                                                                                                                                     >  1:244310/1‑149 (MQ=255)
         tCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTc                                                                                                                           <  2:644402/149‑1 (MQ=255)
               gACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAAt                                                                                                                     >  2:48353/1‑149 (MQ=255)
                  gCTTACCCGTGCTTCAGCCGAGGAAATTCAGGTTCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCTGCCGCGAGCGG‑GTTCGCCAATTCt                                                                                                                  >  2:336944/1‑149 (MQ=255)
                     tAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGGGATTTTGCGTTAAGGAGAAGAGTTAAGGAAAGTAAGTGCCGGATATGCAACACGGCACCTGTCAGACTTAAGGCTGCCCCGCAGCG‑GCGGCTTTCGCCAATTCTAAg                                                                                                               >  2:82244/1‑149 (MQ=255)
                        ccGTGCTTCAGCCGAGGAAATGCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCGCCTGTCAGCATTAAGGCTGCCACGCCGCGAGCGG‑TTTCGCCAATTCTAAGATc                                                                                                            >  2:568911/1‑149 (MQ=255)
                         cGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCACCAATTCTAAGATCt                                                                                                           >  2:263289/1‑149 (MQ=255)
                              ttCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGa                                                                                                      >  2:129491/1‑149 (MQ=255)
                                   ccGAGGAAATTCGGCATCATCAGTGTGAGATTTGGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑GTTCGCCAATGCTAAGATCTTAAGATATgg                                                                                                 >  2:317966/1‑149 (MQ=255)
                                   ccGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATgg                                                                                                 >  2:413019/1‑149 (MQ=255)
                                    cGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATggg                                                                                                >  2:349595/1‑149 (MQ=255)
                                          aaTTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCtttt                                                                                          <  1:129491/149‑1 (MQ=255)
                                             tCAGGATCATCAGTGTAAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGcc                                                                                       <  1:348149/149‑1 (MQ=255)
                                                ggATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTc                                                                                    <  2:446703/149‑1 (MQ=255)
                                                          tgtgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTgcgc                                                                          <  2:512400/149‑1 (MQ=255)
                                                            tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGAt                                                                                                             <  2:416106/112‑1 (MQ=255)
                                                            tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGAt                                                                                                             >  1:416106/1‑112 (MQ=255)
                                                            ggaaaTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCtt                                                                        <  1:321600/145‑1 (MQ=255)
                                                               gaTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGcc                                                                     >  1:539144/1‑149 (MQ=255)
                                                                        ttAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACt                                                            >  2:275805/1‑149 (MQ=255)
                                                                           aGGCGAAGAGTTAAGGAAAGTAAGGGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTccc                                                         <  2:347349/149‑1 (MQ=255)
                                                                           aGGCGAAGAGTCAAGGAATGTAAGTGCCGGAGAAGACCCCCCGCGGCTTGCGGGCTTATTTTGGCGGCGCCGCGGGCGG‑TTTTGCCTATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTccc                                                         <  2:449176/149‑1 (MQ=255)
                                                                             gCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCt                                                       >  2:392686/1‑149 (MQ=255)
                                                                               gAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCg                                                     <  1:349595/149‑1 (MQ=255)
                                                                               gAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCGTGCCGGCACCACTCCCCTCg                                                     >  1:14686/1‑149 (MQ=255)
                                                                                  gagTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                    <  1:547791/131‑1 (MQ=255)
                                                                                  gagTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                    >  2:547791/1‑131 (MQ=255)
                                                                                       aaGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCATTAACGGATGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGt                                             >  1:442266/1‑149 (MQ=255)
                                                                                                  gtGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGc                                  <  2:244310/149‑1 (MQ=255)
                                                                                                   tGCCGGATATGAAATCCGGCAACTGTCAGACTTAAGGCTGCCCCGCCGCGAACGG‑TGTCGCCAATTGTAAGAACTTAAGATATGGGTATTTTGCCATCACAGCAGCGCATGCCAGAAACGCACCCAGCGTGCCGGGTTTAAACGCGGCt                                 >  2:185254/1‑149 (MQ=255)
                                                                                                      cGGATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCa                              >  2:213429/1‑149 (MQ=255)
                                                                                                       ggATATGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCaa                             <  2:30415/149‑1 (MQ=255)
                                                                                                        gATATGAAATCCGCCATCTCTCAGACTTAAGGCTGCCCCGGCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAAc                            <  2:424995/149‑1 (MQ=255)
                                                                                                         atatGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACCATCCCCTCTTGCCGAGTTTAAGCGCGGCTTCAACg                           <  2:463431/149‑1 (MQ=255)
                                                                                                           atGAAATCCGCCACCCGTCAGAGTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTGTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTc                         <  1:265281/149‑1 (MQ=255)
                                                                                                           aggAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGAGCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTc                         <  2:73355/147‑1 (MQ=255)
                                                                                                            tGAAATCCGGCACCTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCAAGTTTAAACGCGGCTTCCACGTcc                        >  1:60186/1‑149 (MQ=255)
                                                                                                                         cTGTCAGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCaa           >  2:555691/1‑149 (MQ=255)
                                                                                                                              aGACTTAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAccc      <  1:213429/149‑1 (MQ=255)
                                                                                                                              aGACTTAAGACTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAccc      >  2:401781/1‑149 (MQ=255)
                                                                                                                                aCTTAAGGCTGCCCCGCCGCGAGAGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAccccc    >  1:562261/1‑147 (MQ=255)
                                                                                                                                  ttAAGGCTGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGccc  >  1:640480/1‑149 (MQ=255)
                                                                                                                                         |                                                                                                                                              
ACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGG‑TTTCGCCAATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCC  >  NC_000913_3_pae_tpiA/4110610‑4110888

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A