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
A7 F28 I1 R1 252 48.5 1661298 98.8% 1641362 138.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,968,268 (C)5→6 coding (167/2247 nt) ptsP ← phosphoenolpyruvate‑protein phosphotransferase PtsP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,968,2631.C97.7% 148.9 / ‑3.2 44coding (172/2247 nt)ptsPphosphoenolpyruvate‑protein phosphotransferase PtsP
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (21/22);  total (22/22)
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

TCTTTTACGGAGGGGATGTATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAG‑CCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCGTGGTG  >  NC_000913/2968124‑2968391
                                                                                                                                             |                                                                                                                                
tcttTTACGGAGGGGATGTATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCATGG‑TTTTTTCAg                                                                                                                                   <  2:398466/140‑1 (MQ=255)
     tACGGAGGGGATGTATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAG‑ccccc                                                                                                                             <  2:221027/140‑1 (MQ=255)
           ggggATGTATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTc                                                                                                                        >  2:31730/1‑140 (MQ=255)
            gggATGTATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCg                                                                                                                       >  1:508355/1‑140 (MQ=255)
                tGTATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCAt                                                                                                                   <  1:31730/140‑1 (MQ=255)
                  tATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCa                                                                                                                 <  1:541277/140‑1 (MQ=255)
                    tttGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAgg                                                                                                               >  2:32531/1‑140 (MQ=255)
                      tGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGgta                                                                                                             >  2:664011/1‑140 (MQ=255)
                        aaGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGgtagt                                                                                                           >  1:261719/1‑140 (MQ=255)
                        aaGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAG‑ccccccgggt                                                                                                                        <  1:168012/126‑6 (MQ=255)
                        aaGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAG‑CCCCCcgggt                                                                                                                        >  2:168012/1‑124 (MQ=255)
                        aaGCTGGGGTGCTTTTGCGCATCTGCAAGGATTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGgtagt                                                                                                           <  2:508355/140‑1 (MQ=255)
                         aGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGgtagta                                                                                                          >  1:809248/1‑140 (MQ=255)
                              gggTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCAt                                                                                                                   <  2:475499/126‑1 (MQ=255)
                              gggTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCAt                                                                                                                   >  1:475499/1‑126 (MQ=255)
                              gggTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTaacaac                                                                                                     <  2:809248/140‑1 (MQ=255)
                              gggTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTaacaac                                                                                                     >  2:236350/1‑140 (MQ=255)
                               ggTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACg                                                                                                    <  1:668164/140‑1 (MQ=255)
                                   cTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGa                                                                                                <  2:721992/140‑1 (MQ=255)
                                        gcgcATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATg                                                                                           <  1:664011/140‑1 (MQ=255)
                                        gcgcATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATg                                                                                           <  2:261719/140‑1 (MQ=255)
                                         cgcATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACg                                                                                                    <  2:183759/130‑1 (MQ=255)
                                         cgcATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACg                                                                                                    >  1:183759/1‑130 (MQ=255)
                                            aTCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCg                                                                                       <  1:150417/140‑1 (MQ=255)
                                                        tATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGAcc                                                                           >  2:617011/1‑140 (MQ=255)
                                                        tATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGAcc                                                                           >  1:30326/1‑140 (MQ=255)
                                                             gTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACa                                                                      <  2:744114/140‑1 (MQ=255)
                                                             gTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACa                                                                      <  1:604155/140‑1 (MQ=255)
                                                                ccGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGAc                                                                   <  1:748840/140‑1 (MQ=255)
                                                                         tGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATc                                                          <  2:691412/140‑1 (MQ=255)
                                                                            cAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCAt                                                       <  1:166174/140‑1 (MQ=255)
                                                                                 aGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCaa                                                  >  1:103043/1‑140 (MQ=255)
                                                                                 aGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCaa                                                  >  1:444142/1‑140 (MQ=255)
                                                                                                  atcaAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAAcc                                 <  1:32306/140‑1 (MQ=255)
                                                                                                    caAACGCGAGCGTTACAGTGCGACCGCGTGGTTTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCa                                >  2:799808/1‑140 (MQ=255)
                                                                                                                      tGCGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCAtt             >  1:43310/1‑140 (MQ=255)
                                                                                                                        cGACCGCGTGG‑TTTTTTCAGCCCCCCGGGTCACCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCa           >  1:262660/1‑140 (MQ=255)
                                                                                                                           ccGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGcc                  <  2:540089/130‑1 (MQ=255)
                                                                                                                           ccGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGcc                  >  1:540089/1‑130 (MQ=255)
                                                                                                                           ccGCGTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGc        >  1:374179/1‑140 (MQ=255)
                                                                                                                            cgcgTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAcgcg       <  1:474332/140‑1 (MQ=255)
                                                                                                                            cgcgTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCg       <  2:374179/140‑1 (MQ=255)
                                                                                                                             gcgTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCgt      >  1:556195/1‑140 (MQ=255)
                                                                                                                              cgTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCgtg     >  2:124548/1‑140 (MQ=255)
                                                                                                                              cgTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCgtg     >  2:737047/1‑140 (MQ=255)
                                                                                                                              cgTGG‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCgtg     <  2:30326/140‑1 (MQ=255)
                                                                                                                                 gg‑TTTTTTCAGCCCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCgtggtg  <  1:124548/140‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                
TCTTTTACGGAGGGGATGTATTTGAAGCTGGGGTGCTTTTGCGCATCTGCAAGGTTTATCGGTTCCGCCAGCCTGCCAACCAGGCCGACGATCCCTTCATCAAACGCGAGCGTTACAGTGCGACCGCGTGG‑TTTTTTCAG‑CCCCCGGGTCGCCATCAGGTAGTAACAACGTCGATCATGATCGGCCAGGTAGACCGAACAGACCTCGGTATCCATCGCAAGACAGATGTCGGTAACCAGAATATTTAACGCCTCATTCAGGCGTGGTG  >  NC_000913/2968124‑2968391

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A