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 F80 I1 R1 83 52.9 1240211 98.2% 1217887 216.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,490,674 Δ1 bp coding (156/564 nt) pabA ← aminodeoxychorismate synthase subunit 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,490,6710G.97.1% 140.3 / ‑1.9 34coding (159/564 nt)pabAaminodeoxychorismate synthase subunit 2
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base . (14/19);  total (14/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.25e-01

CAGCGAATGGTAGCGTGTCACGGTAAGTGGATTTGCCAGCCCCCGAAATACGCCCTCACCGTTATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCACTTTGCTAAA  >  NC_000913/3490440‑3490899
                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                    
caGCGAATGGTAGCGTGTCACGGTAAGTGGATTTGCCAGCCCCCGAAATACGCCCTCACCGTTATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAgg                                                                                                                                                                                                                              >  1:388781/1‑239 (MQ=255)
                                ttGCCAGCCCCCGAAATACGCCCTCACCGTTATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTtg                                                                                                                                                                                                            <  2:429279/225‑1 (MQ=255)
                                     aGCCCCCGAAATACGCCCTCACCGTTATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGatat                                                                                                                                                                                        >  1:599926/1‑240 (MQ=255)
                                                        cACCGTTATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATc                                                                                                                                                                     >  1:294208/1‑240 (MQ=255)
                                                          ccGTTATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGt                                                                                                                                                                   <  2:294201/240‑1 (MQ=255)
                                                              tATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTgcg                                                                                                                                                               <  1:509487/240‑1 (MQ=255)
                                                                  tgtAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATg                                                                                                                                                                                                                       >  2:334388/1‑180 (MQ=255)
                                                                    tAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAAc                                                                                                                                                         <  1:600736/240‑1 (MQ=255)
                                                                       tCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCATGATGACCGAGGCAGACGCCAAAAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAg                                                                                                                                                      >  1:174297/1‑240 (MQ=255)
                                                                            gAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTa                                                                                                                                                           <  1:412263/230‑1 (MQ=255)
                                                                                          cATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATcc                                                                                                                                               >  1:293106/1‑228 (MQ=255)
                                                                                          cATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTc                                                                                                                                    >  1:515567/1‑239 (MQ=255)
                                                                                          cATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTc                                                                                                                                    >  1:24132/1‑239 (MQ=255)
                                                                                                  ttGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGt                                                                                                                            >  2:373871/1‑239 (MQ=255)
                                                                                                        cgcgcACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTAC‑GGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTa                                                                                                                     <  2:124756/240‑1 (MQ=255)
                                                                                                         gcgcACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTa                                                                                                                     <  2:420688/239‑1 (MQ=255)
                                                                                                                                   gcgcCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGt                                                                                           <  2:33417/239‑1 (MQ=255)
                                                                                                                                        aTTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTag                                                                                                                    <  2:307930/209‑1 (MQ=255)
                                                                                                                                        aTTGCCTGATGACCGAAGCAGACGCCAAGAATCGGCAAGCGCCCGTCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTtg                                                                                                                                                                                                            <  2:65887/121‑1 (MQ=255)
                                                                                                                                            ccTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAg                                                                                 <  1:606109/240‑1 (MQ=255)
                                                                                                                                                             aCGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCt                                                                 <  1:464922/239‑1 (MQ=255)
                                                                                                                                                                cgaaGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAg                                                                                                                             <  2:424431/174‑1 (MQ=255)
                                                                                                                                                                  aaGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTagag                                                                                                                  >  1:411274/1‑185 (MQ=255)
                                                                                                                                                                               cgcCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACcgcg                                              <  1:334395/240‑1 (MQ=255)
                                                                                                                                                                                ggccGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGTCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCa                                                                                                                                        <  2:102062/147‑1 (MQ=255)
                                                                                                                                                                                gcCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACcgcg                                              <  1:301739/239‑1 (MQ=255)
                                                                                                                                                                                           tGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCa                                  <  1:45366/240‑1 (MQ=255)
                                                                                                                                                                                                aaTAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGAtt                              >  2:506981/1‑239 (MQ=255)
                                                                                                                                                                                                            ggAGATCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACCAAAg                                                     >  2:51299/1‑204 (MQ=255)
                                                                                                                                                                                                                aTCCCGGCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTAcc             >  2:461604/1‑240 (MQ=255)
                                                                                                                                                                                                                      gCTTCATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAATGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTCTCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCACt          <  1:249573/237‑1 (MQ=255)
                                                                                                                                                                                                                          cATCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCACTTTGCTaa   <  2:64593/240‑1 (MQ=255)
                                                                                                                                                                                                                           aTCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCACTTTGCTaaa  >  1:101449/1‑240 (MQ=255)
                                                                                                                                                                                                                           aTCTGGCGTACA‑GGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCACTTTGCTaa   <  1:238412/239‑1 (MQ=255)
                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                    
CAGCGAATGGTAGCGTGTCACGGTAAGTGGATTTGCCAGCCCCCGAAATACGCCCTCACCGTTATGTGTAATCGGCGAGGTTTTGCCGTGCATGACCTTTGCGGCGCGCACAACTTTACCGCCAAATGCCTGCGCCATTGCCTGATGACCGAGGCAGACGCCAAGAATCGGCAAGCGCCCGGCATAGTGGCGAATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCACTTTGCTAAA  >  NC_000913/3490440‑3490899

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A