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
A10 F44 I1 R1 19 65.8 3201541 96.2% 3079882 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,400,313 A→C D9A (GAT→GCT)  hfq → global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,400,3130AC92.1% 251.5 / 7.0 76D9A (GAT→GCT) hfqglobal sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication
Reads supporting (aligned to +/- strand):  ref base A (5/1);  new base C (40/30);  total (45/31)
Fisher's exact test for biased strand distribution p-value = 3.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATC  >  NC_000913/4400217‑4400408
                                                                                                |                                                                                               
gaCGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTcc                                                                                              >  2:263363/1‑100 (MQ=255)
gaCGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTcc                                                                                              >  2:1156293/1‑100 (MQ=255)
gaCGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTcc                                                                                              >  1:246939/1‑100 (MQ=255)
gaCGTATCGTGCACAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTcc                                                                                              >  1:848553/1‑100 (MQ=255)
 aCGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCg                                                                                             <  1:1485231/100‑1 (MQ=255)
  cGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGt                                                                                            >  2:827849/1‑100 (MQ=255)
     tccgatctcAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTcc                                                                                         <  1:698935/92‑1 (MQ=255)
     aTCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTcc                                                                                         <  1:496689/100‑1 (MQ=255)
      tagTGCTCAATTTTTTCATAATAGAAATGTTGAAAGTATAAATAAGCATATAAGGAAAAGAGAGAATTGCTAAGGGTCAATCTTTACAAGCTCCGTTcc                                                                                         <  1:683379/97‑1 (MQ=255)
       cGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATcggaagagc                                                                                       >  2:709940/1‑92 (MQ=255)
       cGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTg                                                                                       >  1:806512/1‑100 (MQ=255)
          gcgcAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAAc                                                                                    >  1:1343075/1‑100 (MQ=255)
           cgcAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACg                                                                                   >  1:1018146/1‑100 (MQ=255)
            gcAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGc                                                                                  >  1:1020386/1‑100 (MQ=255)
             cAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTccagatcgga                                                                                 >  2:698941/1‑92 (MQ=255)
             cAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCa                                                                                 >  1:226221/1‑100 (MQ=255)
                ttttttCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTg                                                                              <  1:435469/100‑1 (MQ=255)
                ttttttCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTg                                                                              <  2:811477/100‑1 (MQ=255)
                      cAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCgg                                                                        >  2:783110/1‑100 (MQ=255)
                      cAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCgg                                                                        <  1:791614/100‑1 (MQ=255)
                      cAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCgg                                                                        <  1:771010/100‑1 (MQ=255)
                       aGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGACAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTGCCTGAACGCACTGCGTCggg                                                                       <  1:171688/100‑1 (MQ=255)
                        gAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGa                                                                      >  1:484115/1‑100 (MQ=255)
                           tCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACg                                                                   >  2:1432498/1‑100 (MQ=255)
                           tCGAAAGGTTCAAAGTACAAATAACCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAAc                                                                    <  1:212897/99‑1 (MQ=255)
                            cGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACgt                                                                  >  1:743208/1‑100 (MQ=255)
                             gAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACgtg                                                                 >  1:353373/1‑100 (MQ=255)
                             gAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTACGTTAATGAACGAACTGCGTCGCGAACg                                                                   >  1:550242/1‑98 (MQ=255)
                              aaaGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACgtgt                                                                <  2:173751/100‑1 (MQ=255)
                                aGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTc                                                              <  1:1059055/100‑1 (MQ=255)
                                 ggTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTcc                                                             >  2:281064/1‑100 (MQ=255)
                                 ggTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTACGTTACTAAACGCACTGCGTCGGGAACGTGTTcc                                                             >  1:1593157/1‑100 (MQ=255)
                                   ttCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAg                                                           >  1:1091535/1‑100 (MQ=255)
                                     cAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGtt                                                         >  2:1210833/1‑100 (MQ=255)
                                      aaaaTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGttt                                                        >  1:803928/1‑100 (MQ=255)
                                      aaaGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGttt                                                        <  2:648317/100‑1 (MQ=255)
                                        aGTACAAAGAAGCATATAAGGAAAAGAGAGAATCGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCt                                                      <  1:1291525/100‑1 (MQ=255)
                                          tACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCtat                                                    <  2:966687/100‑1 (MQ=255)
                                           aCAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCtatt                                                   <  2:848560/100‑1 (MQ=255)
                                            cAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCtattt                                                  >  2:1025108/1‑100 (MQ=255)
                                            cAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCtattt                                                  >  1:1524373/1‑100 (MQ=255)
                                             aaaTAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCtattta                                                 <  2:1448742/100‑1 (MQ=255)
                                                 aaGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTg                                             <  2:1344355/100‑1 (MQ=255)
                                                    cATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTg                                          <  1:662124/100‑1 (MQ=255)
                                                      tataAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGaa                                        >  1:553048/1‑100 (MQ=255)
                                                        taAGGAAAAGAGCGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGCACGCACTGCGTCGGGAACGTGTTCCCGTTTCTATTTATTTGGTGaacg                                      >  1:66636/1‑98 (MQ=255)
                                                        taAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATg                                      >  2:628378/1‑100 (MQ=255)
                                                        taAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATg                                      >  1:354802/1‑100 (MQ=255)
                                                        taAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATg                                      >  2:968142/1‑100 (MQ=255)
                                                         aaGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATgg                                     >  2:1475108/1‑100 (MQ=255)
                                                         aaGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATgg                                     <  2:353376/100‑1 (MQ=255)
                                                           ggAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTa                                   >  2:1043251/1‑100 (MQ=255)
                                                             aaaaGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTAtt                                 >  2:682240/1‑100 (MQ=255)
                                                              aaaGAGAGAATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTa                                <  1:758898/100‑1 (MQ=255)
                                                                 gagagaATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGc                             >  2:1582201/1‑100 (MQ=255)
                                                                   gagaATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTg                           >  1:584447/1‑100 (MQ=255)
                                                                    agaATGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGc                          <  2:220965/100‑1 (MQ=255)
                                                                     gaATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTGTATTTATGTGGTGAATGGTATTAAGCTGCa                         >  2:205662/1‑100 (MQ=255)
                                                                        tGGCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAgg                      <  2:33270/100‑1 (MQ=255)
                                                                          gCTAAGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGc                    >  2:1234002/1‑100 (MQ=255)
                                                                           cTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGGACTGCGTCGTTAACGTGTTCCAGTTTCTACTTATTTGGTCAATGGTATTCAGCAGCAAtgg                     >  1:224342/1‑98 (MQ=255)
                                                                             aaGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCaaa                 >  2:1304957/1‑100 (MQ=255)
                                                                             aaGGGGCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCaaa                 >  1:457779/1‑100 (MQ=255)
                                                                                gggCAATCTTTACAAGCTCCGTTCCTGAACGCCCTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCg              <  2:380580/100‑1 (MQ=255)
                                                                                gggCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCg              <  1:1166317/100‑1 (MQ=255)
                                                                                 ggCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGa             >  2:683068/1‑100 (MQ=255)
                                                                                 ggCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGa             >  2:683076/1‑100 (MQ=255)
                                                                                  gCAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAg            <  1:364419/100‑1 (MQ=255)
                                                                                   cAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGt           >  2:1272127/1‑100 (MQ=255)
                                                                                   cAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGt           <  1:1298755/100‑1 (MQ=255)
                                                                                   cAATCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGt           <  1:1416394/100‑1 (MQ=255)
                                                                                    aaTCTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTc          >  2:403890/1‑100 (MQ=255)
                                                                                       cTTTACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCttt       <  1:1277914/100‑1 (MQ=255)
                                                                                          tACAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGa    <  2:226224/100‑1 (MQ=255)
                                                                                          tACAAGCTCCGTTCCTAAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGATGCAAGGGCAAATCGAGTCTTTTGa    <  2:632981/100‑1 (MQ=255)
                                                                                            cAAGCTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATc  >  2:100685/1‑100 (MQ=255)
                                                                                                |                                                                                               
GACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATC  >  NC_000913/4400217‑4400408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A