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
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,880,851 T→A 9.5% intergenic (‑92/+35) leuE ← / ← dmlR leucine efflux protein/transcriptional activator of dmlA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,880,8510TA 9.5% 208.8 / 10.3 63intergenic (‑92/+35)leuE/dmlRleucine efflux protein/transcriptional activator of dmlA
Reads supporting (aligned to +/- strand):  ref base T (28/29);  new base A (3/3);  total (31/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

AATGGCCCCAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGT  >  NC_000913/1880706‑1880972
                                                                                                                                                 |                                                                                                                         
aaTGGCCCCAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTa                                                                                                                         <  4:740493/148‑1 (MQ=255)
     ccccAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTg                                                                                                                    <  3:197084/148‑1 (MQ=255)
          aCCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATc                                                                                                               >  2:346467/1‑148 (MQ=255)
                        gTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGat                                                                                                                  >  2:310251/1‑131 (MQ=255)
                        gTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGat                                                                                                                  <  1:310251/131‑1 (MQ=255)
                             tCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAAt                                                                                                    >  2:916140/1‑140 (MQ=255)
                             tCAGAACCCCGTATTCAGCGAACACATTAACCTCATTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCTATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAAt                                                                                                    <  1:916140/140‑1 (MQ=255)
                                 aaCCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAAt                                                                                        <  1:346467/148‑1 (MQ=255)
                                                 aaCACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGaa                                                                                                >  1:757755/1‑124 (MQ=255)
                                                 aaCACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGaa                                                                                                <  2:757755/124‑1 (MQ=255)
                                                 aaCACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGaa                                                                                                <  2:109948/124‑1 (MQ=255)
                                                 aaCACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGaa                                                                                                >  1:109948/1‑124 (MQ=255)
                                                      aTTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGaa                                                                                                <  1:340234/119‑1 (MQ=255)
                                                      aTTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGaa                                                                                                >  2:340234/1‑119 (MQ=255)
                                                       ttAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTa                                                                                                                         <  4:587589/93‑1 (MQ=255)
                                                       ttAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTa                                                                                                                         >  3:587589/1‑93 (MQ=255)
                                                             tctTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGat                                                                                                                  >  2:280218/1‑94 (MQ=255)
                                                             tctTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTAAAACCTGat                                                                                                                  <  1:280218/94‑1 (MQ=255)
                                                                    ttATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAg                                                                          <  4:407201/127‑1 (MQ=255)
                                                                    ttATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAg                                                                          >  3:407201/1‑127 (MQ=255)
                                                                    ttATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTc                                                     >  2:370054/1‑148 (MQ=255)
                                                                      aTCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAAc                                                                                                            >  1:269022/1‑91 (MQ=255)
                                                                      aTCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAAc                                                                                                            <  2:269022/91‑1 (MQ=255)
                                                                          ttCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGtttt                                                                                                                          <  3:636263/73‑1 (MQ=255)
                                                                          ttCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGtttt                                                                                                                          >  4:636263/1‑73 (MQ=255)
                                                                               tCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAAtt                                                                 >  1:25470/1‑125 (MQ=255)
                                                                               tCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAAtt                                                                 <  2:25470/125‑1 (MQ=255)
                                                                                 aTGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTgg                                        <  1:370054/148‑1 (MQ=255)
                                                                                                tGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCa                                                                                             <  3:1116537/80‑1 (MQ=255)
                                                                                                tGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCa                                                                                             >  4:1116537/1‑80 (MQ=255)
                                                                                                tGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCt                            >  4:1017243/1‑145 (MQ=255)
                                                                                                tGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCt                            <  3:1017243/145‑1 (MQ=255)
                                                                                                  aaTATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTaa                                   <  4:10381/136‑1 (MQ=255)
                                                                                                  aaTATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTaa                                   >  3:10381/1‑136 (MQ=255)
                                                                                                          aaCCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCg                                                               <  2:1080958/100‑1 (MQ=255)
                                                                                                          aaCCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCg                                                               >  1:1080958/1‑100 (MQ=255)
                                                                                                          aaCCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAAt                               <  4:906505/132‑1 (MQ=255)
                                                                                                          aaCCAATCTGTAGCGGCTCAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAAt                               >  3:906505/1‑132 (MQ=255)
                                                                                                              aaTCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAAtt                              >  4:538355/1‑129 (MQ=255)
                                                                                                              aaTCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAAtt                              <  3:538355/129‑1 (MQ=255)
                                                                                                                 cTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCa                                                                                                              <  2:625326/46‑1 (MQ=255)
                                                                                                                 cTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCa                                                                                                              >  1:625326/1‑46 (MQ=255)
                                                                                                                 cTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAAtt                                                                 >  3:1072007/1‑91 (MQ=255)
                                                                                                                 cTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAAtt                                                                 <  4:1072007/91‑1 (MQ=255)
                                                                                                                       cGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGt  >  1:1042849/1‑148 (MQ=255)
                                                                                                                       cGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGt  <  1:151083/148‑1 (MQ=255)
                                                                                                                       cGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGt  >  1:392948/1‑148 (MQ=255)
                                                                                                                           ttAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAAt                               >  2:216326/1‑115 (MQ=255)
                                                                                                                           ttAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAAt                               <  1:216326/115‑1 (MQ=255)
                                                                                                                            tAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTg      <  2:241229/139‑1 (MQ=255)
                                                                                                                            tAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTg      >  1:241229/1‑139 (MQ=255)
                                                                                                                               aaaGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCg                                                               >  3:776409/1‑79 (MQ=255)
                                                                                                                               aaaGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCg                                                               <  4:776409/79‑1 (MQ=255)
                                                                                                                               aaaGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACt                                          >  4:683508/1‑100 (MQ=255)
                                                                                                                               aaaGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACt                                          <  3:683508/100‑1 (MQ=255)
                                                                                                                                aaGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGa     <  1:482438/136‑1 (MQ=255)
                                                                                                                                aaGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGa     >  2:482438/1‑136 (MQ=255)
                                                                                                                                    agaAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCATGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCg         <  3:772444/128‑1 (MQ=255)
                                                                                                                                    agaAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCg         >  4:772444/1‑128 (MQ=255)
                                                                                                                                      aaaaTCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGt  <  3:505292/133‑1 (MQ=255)
                                                                                                                                      aaaaTCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGt  >  4:505292/1‑133 (MQ=255)
                                                                                                                                          tCAGGTTAAAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCaaa                                               >  1:489806/1‑84 (MQ=255)
                                                                                                                                          tCAGGTTAAAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCaaa                                               <  2:489806/84‑1 (MQ=255)
                                                                                                                                           cAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTgg                                        >  2:481907/1‑90 (MQ=255)
                                                                                                                                           cAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTgg                                        <  1:481907/90‑1 (MQ=255)
                                                                                                                                               ttttAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCg                                                               <  1:952883/63‑1 (MQ=255)
                                                                                                                                               ttttAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCg                                                               >  2:952883/1‑63 (MQ=255)
                                                                                                                                                 |                                                                                                                         
AATGGCCCCAACCAGATAGGTCCAGTAATTCAGAACCCCGTATTCAGCGAACACATTAACCTCTTTAATTATCTTTCGATCATGCGCGATTAAAGGTGAATATGCTAACCAATCTGTAGCGGCTTAGAAAGGAGAAAATCAGGTTTTAACCTGATATCAACCCGATAATTGAATCATTAATCAGGCATGCTCCAGTGAAAAATTCGGGTAGTGCTCGGCAAAATACTGGCGTAAAAATTCTACCGTTATCCGCACTTTCGCTGACGT  >  NC_000913/1880706‑1880972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A