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
A3 F50 I2 R1 257 49.9 1554294 99.0% 1538751 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,296,292 C→T R162C (CGC→TGC)  diaA → DnaA initiator‑associating factor for replication initiation

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,296,2920CT98.0% 186.3 / NA 50R162C (CGC→TGC) diaADnaA initiator‑associating factor for replication initiation
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (22/27);  total (22/28)
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

AGCCATTTCCACCCGTGGCAACAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCCGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCATTATCGCCAATCGCAGTCCT  >  NC_000913/3296150‑3296437
                                                                                                                                              |                                                                                                                                                 
aGCCATTTCCACCCGTGGCAACAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCt                                                                                                                                           <  2:760981/151‑1 (MQ=255)
aGCCATTTCCACCCGTGGCAACAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCCATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCt                                                                                                                                           >  2:103155/1‑151 (MQ=255)
          aCCCGTGGCAACAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGt                                                                                                                                  >  1:502730/1‑150 (MQ=255)
             cGTGGCACCAGCCGCGATATTGTTAAAGCAGTTGAGGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGTCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCAt                                                                                                                                     <  1:454699/144‑1 (MQ=255)
               tGGCAACAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCt                                                                                                                            >  1:232416/1‑151 (MQ=255)
                     cAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCAtt                                                                                                                      <  2:530793/151‑1 (MQ=255)
                     cAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCAtt                                                                                                                      >  2:180682/1‑151 (MQ=255)
                         cgcgATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAgg                                                                                                                  >  1:613882/1‑151 (MQ=255)
                             atatTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAAt                                                                                                              >  1:484346/1‑151 (MQ=255)
                              tatTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAAt                                                                                                              <  1:107259/150‑1 (MQ=255)
                                ttGTTAAAGCAGTTAAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGAATTCAGGaa                                                                                                                <  1:583902/146‑1 (MQ=255)
                                  gTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCat                                                                                                          <  2:580333/150‑1 (MQ=255)
                                         cAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGAc                                                                                                  <  2:684916/151‑1 (MQ=255)
                                           gTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACgg                                                                                                <  2:484398/151‑1 (MQ=255)
                                             tGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGt                                                                                               <  2:688868/150‑1 (MQ=255)
                                               aaGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTaaa                                                                                            <  1:773253/151‑1 (MQ=255)
                                                aGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTaaa                                                                                            >  1:620720/1‑150 (MQ=255)
                                                 gccgccGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAAtt                                                                                          <  2:711825/151‑1 (MQ=255)
                                                 gccgccGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAAt                                                                                           <  2:759488/150‑1 (MQ=255)
                                                  ccgccgTTACGCGTGATATTAACATTGTGGCATTGACCGGCTATGACGGCGGCTAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCTCATCGTAGTGCTCGCATTCAGGAAAGGCATCTGCTGACGGTAAATTg                                                                                         <  1:179085/151‑1 (MQ=255)
                                                          aCGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCg                                                                                 <  1:357539/151‑1 (MQ=255)
                                                                gATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGa                                                                           <  2:575456/151‑1 (MQ=255)
                                                                     gACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGa                                                                       <  1:335357/150‑1 (MQ=255)
                                                                         aTTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAac                                                                   >  2:330413/1‑150 (MQ=255)
                                                                             tgGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCt                                                              >  2:520322/1‑151 (MQ=255)
                                                                                      ccGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTc                                                      >  2:530824/1‑150 (MQ=255)
                                                                                      ccGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCa                                                     <  2:698359/151‑1 (MQ=255)
                                                                                       cGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCAc                                                    >  2:483228/1‑151 (MQ=255)
                                                                                        ggCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCAcc                                                   >  1:377087/1‑151 (MQ=255)
                                                                                           tATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAgg                                                >  2:568984/1‑151 (MQ=255)
                                                                                            aTGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAgg                                                <  1:403056/150‑1 (MQ=255)
                                                                                            aTGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAgg                                                <  2:520159/150‑1 (MQ=255)
                                                                                              gACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGgatg                                             <  1:12162/151‑1 (MQ=255)
                                                                                                  gcggcgAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGAtt                                          >  1:735088/1‑150 (MQ=255)
                                                                                                   cggcgAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTa                                         >  2:150628/1‑150 (MQ=255)
                                                                                                    ggcgAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAg                                       <  2:663647/151‑1 (MQ=255)
                                                                                                      cgAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAgg                                      >  2:536102/1‑150 (MQ=255)
                                                                                                      cgAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGga                                     <  1:540166/151‑1 (MQ=255)
                                                                                                         aCTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGgaga                                   >  2:567131/1‑150 (MQ=255)
                                                                                                            tGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATa                                <  2:243111/150‑1 (MQ=255)
                                                                                                            tGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATAc                               >  1:23169/1‑151 (MQ=255)
                                                                                                             gCAGGTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACa                              <  2:11675/151‑1 (MQ=255)
                                                                                                                ggTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATg                            >  2:14090/1‑150 (MQ=255)
                                                                                                                ggTTTGTTAGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATg                            >  2:243929/1‑150 (MQ=255)
                                                                                                                        aGGGCCACAGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCAtt                    <  2:503861/150‑1 (MQ=255)
                                                                                                                             cacaGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCATTATCGcc              <  2:138826/151‑1 (MQ=255)
                                                                                                                              acaGGATGTGGAGATCTGTATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCATTATCGcc              >  2:249363/1‑150 (MQ=255)
                                                                                                                              acaGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCATTATCGCCa             <  1:542828/151‑1 (MQ=255)
                                                                                                                               caGGATGTGGAGATCTGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCATTATCGCCa             >  2:433442/1‑150 (MQ=255)
                                                                                                                                         agaTCCGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCATTATCGCCAATCGCAGTCCt  <  2:563255/151‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                                 
AGCCATTTCCACCCGTGGCAACAGCCGCGATATTGTTAAAGCAGTTGAAGCCGCCGTTACGCGTGATATGACCATTGTGGCATTGACCGGCTATGACGGCGGCGAACTTGCAGGTTTGTTAGGGCCACAGGATGTGGAGATCCGCATTCCTTCGCATCGTAGTGCTCGCATTCAGGAAATGCATATGCTGACGGTAAATTGCCTGTGCGATCTGATCGATAACACGCTTTTCCCTCACCAGGATGATTAAGGAGAATACATGAAGGCATTATCGCCAATCGCAGTCCT  >  NC_000913/3296150‑3296437

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A