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 I1 R1 300 54.7 1718999 98.4% 1691495 149.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,740,507 T→C Q215R (CAG→CGG)  aroF ← 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,740,5070TC98.0% 179.1 / NA 51Q215R (CAG→CGG) aroF3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (24/26);  minor base A (1/0);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

ATCAGAGACGGGCGCAGTCCCGCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCTGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGT  >  NC_000913/2740360‑2740652
                                                                                                                                                   |                                                                                                                                                 
aTCAGAGACGGGCGCAGTCCCGCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGt                                                                                                                                                >  2:82133/1‑151 (MQ=255)
aTCAGAGACGGGCGCAGTCCCGCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGt                                                                                                                                                >  2:551293/1‑151 (MQ=255)
   agagACGGGCGCAGTCCCGCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTa                                                                                                                                              >  2:49167/1‑150 (MQ=255)
     agaCGGGCGCAGTCCCGCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATg                                                                                                                                           >  1:21824/1‑151 (MQ=255)
       aCGGGCGCAGCCCCTCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCTTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATg                                                                                                                                           <  2:501594/149‑1 (MQ=255)
                  cccGCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGt                                                                                                                              <  2:855412/151‑1 (MQ=255)
                     gCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCg                                                                                                                           <  1:449745/151‑1 (MQ=255)
                       cTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGc                                                                                                                         >  2:345213/1‑151 (MQ=255)
                        tGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCt                                                                                                                        >  2:177211/1‑151 (MQ=255)
                         gTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCt                                                                                                                        <  1:647449/150‑1 (MQ=255)
                         gTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCt                                                                                                                        <  1:403915/150‑1 (MQ=255)
                         gTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTg                                                                                                                       <  1:815597/151‑1 (MQ=255)
                                ctctTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGggc                                                                                                                    <  1:738381/147‑1 (MQ=255)
                                ctctTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGggc                                                                                                                    >  2:738424/1‑147 (MQ=255)
                                 tctTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGggcggcgg                                                                                                               >  1:838268/1‑151 (MQ=255)
                                        cacaTTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCa                                                                                                         <  2:393008/150‑1 (MQ=255)
                                         acaTTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATa                                                                                                       <  2:316011/151‑1 (MQ=255)
                                         acaTTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATa                                                                                                       <  1:658076/151‑1 (MQ=255)
                                               cgcAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTa                                                                                                 <  2:790912/151‑1 (MQ=255)
                                               cgcAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGATGGGCGGCGGCGCGCATAGCGTTa                                                                                                 <  2:18099/151‑1 (MQ=255)
                                                gcAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTaa                                                                                                <  1:717776/151‑1 (MQ=255)
                                                   aCATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTg                                                                                             <  1:783652/151‑1 (MQ=255)
                                                    cATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTg                                                                                             <  1:741113/150‑1 (MQ=255)
                                                       ccGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCACCCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTg                                                                                          <  1:416162/150‑1 (MQ=255)
                                                       ccGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTg                                                                                          <  1:705682/150‑1 (MQ=255)
                                                          cAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGc                                                                                      >  1:248301/1‑151 (MQ=255)
                                                          cAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGc                                                                                      >  1:226884/1‑151 (MQ=255)
                                                           aGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGcc                                                                                     >  1:707954/1‑151 (MQ=255)
                                                           aGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCAGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGtt                                                                                        >  1:745421/1‑148 (MQ=255)
                                                                   aGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGc                                                                              <  2:270055/150‑1 (MQ=255)
                                                                       cGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCg                                                                         <  1:383250/151‑1 (MQ=255)
                                                                        ggCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCgg                                                                        >  1:13334/1‑151 (MQ=255)
                                                                        ggCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGACAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGACGTCgg                                                                        <  1:610587/151‑1 (MQ=255)
                                                                           gcTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGc                                                                     <  1:36623/151‑1 (MQ=255)
                                                                             tttACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCg                                                                   >  1:449359/1‑151 (MQ=255)
                                                                                      gcgcAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTaaaa                                                          <  2:34118/151‑1 (MQ=255)
                                                                                        gcAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAaacc                                                        >  1:277723/1‑151 (MQ=255)
                                                                                            gATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAaaccaacc                                                    >  2:380697/1‑151 (MQ=255)
                                                                                             aTCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCg                                                   >  1:255674/1‑151 (MQ=255)
                                                                                                   tGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATgg                                             >  1:407775/1‑151 (MQ=255)
                                                                                                    ggCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGa                                            <  1:436506/151‑1 (MQ=255)
                                                                                                            ggATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCgg                                    >  1:45893/1‑151 (MQ=255)
                                                                                                               ttCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAgg                                 >  2:394654/1‑151 (MQ=255)
                                                                                                                  cccTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCa                              <  1:101806/151‑1 (MQ=255)
                                                                                                                    cTGAGTTTGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCAtt                            >  1:510166/1‑151 (MQ=255)
                                                                                                                         tttGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACg                       >  1:311710/1‑151 (MQ=255)
                                                                                                                          ttGTAGCAACGCAACCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACgg                      >  2:369233/1‑151 (MQ=255)
                                                                                                                                    gcaacCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCg            >  1:35787/1‑151 (MQ=255)
                                                                                                                                    gcaacCTGCCCTGCCCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCg            <  2:26619/151‑1 (MQ=255)
                                                                                                                                            ccctgccCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGtt    <  1:394622/151‑1 (MQ=255)
                                                                                                                                            ccctgccCGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGtt    >  1:761395/1‑151 (MQ=255)
                                                                                                                                               tgcccgGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCTCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTCTg              >  2:367918/1‑138 (MQ=255)
                                                                                                                                               tgcccgGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCTCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTCTg              <  1:367895/138‑1 (MQ=255)
                                                                                                                                               tgcccgGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGt  >  2:660035/1‑150 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
ATCAGAGACGGGCGCAGTCCCGCCTGTTCCATCTCTTTTTCACATTGCGCAACATCCGCAGGGCTATAGTTCGGCGCTTTACCACCGCGCAGGATCACATGGCCGTCCGGATTCCCCTGAGTTTGTAGCAACGCAACCTGCCCTGCCTGGTTAATGCCAACAAAACGGTGCGGCTGGGCGGCGGCGCGCATAGCGTTAATTGCTGTTGCCAGACTGCCGTCGGTGCCGTTTTTAAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGT  >  NC_000913/2740360‑2740652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A