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
A20 F48 I1 R1 52 61.9 2103308 98.8% 2078068 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,554,444 C→A L454M (CTG→ATG)  malT → DNA‑binding transcriptional activator MalT

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,554,4440CA98.2% 191.3 / ‑2.6 55L454M (CTG→ATG) malTDNA‑binding transcriptional activator MalT
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (31/23);  total (32/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.64e-01

AGTTGGTGTTATTGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTGCTGGGTGAAGTGCTG  >  NC_000913/3554313‑3554578
                                                                                                                                   |                                                                                                                                      
aGTTGGTGTTATTGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGcc                                                                                                                                <  1:1028877/140‑1 (MQ=255)
aGTTGGTGTTATTGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGcc                                                                                                                                >  2:423205/1‑140 (MQ=255)
            tGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGAtt                                                                                                                    <  2:746432/140‑1 (MQ=255)
               aGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAAc                                                                                                                 <  1:787442/140‑1 (MQ=255)
                ggCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACg                                                                                                                >  2:401839/1‑140 (MQ=255)
                  cGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGcc                                                                                                                                >  1:107567/1‑122 (MQ=255)
                  cGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGcc                                                                                                                                <  2:107567/122‑1 (MQ=255)
                    tGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATgg                                                                                                            <  1:102163/140‑1 (MQ=255)
                    tGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATgg                                                                                                            >  2:1024387/1‑140 (MQ=255)
                      gCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTa                                                                                                          >  1:40719/1‑140 (MQ=255)
                       cTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTaa                                                                                                         <  1:619052/140‑1 (MQ=255)
                           tGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCg                                                                                                     >  2:366992/1‑140 (MQ=255)
                               aaGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATg                                                                                                 <  1:401839/140‑1 (MQ=255)
                                     aCATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCgg                                                                                           >  2:458974/1‑140 (MQ=255)
                                            tACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCt                                                                                    >  2:28145/1‑140 (MQ=255)
                                            tACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCt                                                                                    >  2:632471/1‑140 (MQ=255)
                                                     gTTAACTCTCTGCTAGCTCGTGCTGAACATGACATCAAGGACATCAGAGAAGACACCATGGATGCAGAATTTAAAGCTATGCGCGCCAAGGTGGCGATTAACGATGATAATCCGGATGAAGCGGAACGGCTGCCAAAACt                                                                           >  2:512994/1‑140 (MQ=255)
                                                     gTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACt                                                                           <  1:973379/140‑1 (MQ=255)
                                                          cacCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCAc                                                                      <  1:632471/140‑1 (MQ=255)
                                                               tGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCATGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGaa                                                                 >  1:631208/1‑140 (MQ=255)
                                                               tGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGACCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGaa                                                                 >  1:1013159/1‑140 (MQ=255)
                                                                    gCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCt                                                            >  2:907724/1‑140 (MQ=255)
                                                                         tGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTgccgc                                                       >  2:144865/1‑140 (MQ=255)
                                                                         tGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTgccgc                                                       >  2:32950/1‑140 (MQ=255)
                                                                         tGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTgccgc                                                       <  1:82636/140‑1 (MQ=255)
                                                                         tGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTgccgc                                                       >  1:889599/1‑140 (MQ=255)
                                                                              aaCATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGc                                                  >  1:594248/1‑140 (MQ=255)
                                                                              aaCATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGc                                                  >  1:384045/1‑140 (MQ=255)
                                                                              aaCATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTAGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGc                                                  <  1:277898/140‑1 (MQ=255)
                                                                               aCATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCt                                                 <  2:86493/140‑1 (MQ=255)
                                                                                           ggACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGcc                                     <  1:1024387/140‑1 (MQ=255)
                                                                                                tCAGAGAAGACACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCAtt                                <  2:40719/140‑1 (MQ=255)
                                                                                                     gaagaCACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGc                           <  2:269164/140‑1 (MQ=255)
                                                                                                      aagaCACCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCa                          >  2:872848/1‑140 (MQ=255)
                                                                                                         acacCATGCACGCAGAGTTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAAcc                       >  1:380424/1‑140 (MQ=255)
                                                                                                         acacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAAcc                       >  1:600030/1‑140 (MQ=255)
                                                                                                         acacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAAcc                       >  1:934656/1‑140 (MQ=255)
                                                                                                         acacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAAcc                       >  2:179753/1‑140 (MQ=255)
                                                                                                         acacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAAcc                       >  1:386759/1‑140 (MQ=255)
                                                                                                         acacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTCGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAAct                       >  2:390053/1‑139 (MQ=255)
                                                                                                         acacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTAGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAAcc                       >  1:740854/1‑140 (MQ=255)
                                                                                                          cacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCt                      <  1:32950/140‑1 (MQ=255)
                                                                                                          aacCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCt                      <  2:384045/139‑1 (MQ=255)
                                                                                                           acCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTc                     >  1:1038061/1‑140 (MQ=255)
                                                                                                           acCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTc                     >  1:398971/1‑140 (MQ=255)
                                                                                                           acCATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGATCTATAGCCGCATTGTGGCAACCTc                     >  1:691602/1‑140 (MQ=255)
                                                                                                             cATGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCgg                   >  2:47642/1‑140 (MQ=255)
                                                                                                              aTGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGt                  >  1:652368/1‑140 (MQ=255)
                                                                                                              aTGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGt                  >  1:398429/1‑140 (MQ=255)
                                                                                                               tgcatgcaGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTg                 <  2:631208/140‑1 (MQ=255)
                                                                                                               tGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTg                 <  1:264243/140‑1 (MQ=255)
                                                                                                               tGCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTg                 <  1:144865/140‑1 (MQ=255)
                                                                                                               tGCACGCAGAATTTAACGCTATGCGCGACCAGGTGGAGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAGGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTg                 <  2:889599/140‑1 (MQ=255)
                                                                                                                gCACGCAGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTGc                >  1:520421/1‑140 (MQ=255)
                                                                                                                      agagTTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTGCTGGGTg          <  2:380424/140‑1 (MQ=255)
                                                                                                                      aGAATTTAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTGCTGGGTg          <  1:458974/140‑1 (MQ=255)
                                                                                                                           ttAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTGCTGGGTGAAGtg     <  2:740854/140‑1 (MQ=255)
                                                                                                                           ttAACGCTATGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTGCTGGGTGAAGtg     <  2:934656/140‑1 (MQ=255)
                                                                                                                              aCGCTATGCGCGACCAGGTCGCGATTAACGATGGTAATCCGGATGAGGCGGAACGCCCGGCCAAACTGGCACTGGAAGAGATGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCACCCTGGGTGCTGGGTGAAGtgctg  <  2:594248/140‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                      
AGTTGGTGTTATTGCAGGCGTGGCTGATGCAAAGCCAACATCGCTACGGCGAAGTTAACACCCTGCTAGCCCGTGCTGAACATGAAATCAAGGACATCAGAGAAGACACCATGCACGCAGAATTTAACGCTCTGCGCGCCCAGGTGGCGATTAACGATGGTAATCCGGATGAAGCGGAACGGCTGGCAAAACTGGCACTGGAAGAGCTGCCGCCGGGCTGGTTCTATAGCCGCATTGTGGCAACCTCGGTGCTGGGTGAAGTGCTG  >  NC_000913/3554313‑3554578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A