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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 375,307 C→T intergenic (+426/‑152) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913375,3070CT100.0% 176.4 / NA 55intergenic (+426/‑152)mhpE/mhpT4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/29);  total (26/29)

GCGCGAGAATTTGTAGGCCTGATAAGACGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGCGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCAATGTATCAGTCGCGATTCACCTGCACTC  >  NC_000913/375171‑375441
                                                                                                                                        |                                                                                                                                      
gcgcGAGAATTTGTAGGCCTGATAAGACGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAgtgt                                                                                                                                      >  2:256012/1‑139 (MQ=38)
                      tAAGACGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGa                                                                                                                <  1:1391787/139‑1 (MQ=37)
                          aCGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAgtgt                                                                                                                                      >  1:290980/1‑113 (MQ=18)
                          aCGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAgtgt                                                                                                                                      <  2:290980/113‑1 (MQ=17)
                          aCGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGc                                                                                                            >  2:445793/1‑139 (MQ=25)
                          aCGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGc                                                                                                            >  1:1341043/1‑139 (MQ=25)
                              gTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGa                                                                                                        >  2:1533373/1‑139 (MQ=37)
                                      cGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATaa                                                                                                >  1:1390576/1‑139 (MQ=38)
                                                aTCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTc                                                                                      >  2:1360587/1‑139 (MQ=255)
                                                 tCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTcc                                                                                     <  2:755562/139‑1 (MQ=255)
                                                     cgcACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGcc                                                                                 <  1:759299/139‑1 (MQ=255)
                                                     cgcACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGcc                                                                                 >  1:448724/1‑139 (MQ=255)
                                                          gACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACAt                                                                            <  1:256012/139‑1 (MQ=255)
                                                               ccGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATg                                                                                                      <  1:1382614/108‑1 (MQ=255)
                                                               ccGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATg                                                                                                      >  2:1382614/1‑108 (MQ=255)
                                                                    tGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTa                                                                  >  2:1446397/1‑139 (MQ=255)
                                                                      cggcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAgg                                                                <  2:1341043/139‑1 (MQ=255)
                                                                      cggcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAgg                                                                >  2:254588/1‑139 (MQ=255)
                                                                       ggcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCgg                                                                                                         <  2:491738/97‑1 (MQ=255)
                                                                       ggcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCgg                                                                                                         >  1:491738/1‑97 (MQ=255)
                                                                       ggcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               <  1:254588/139‑1 (MQ=255)
                                                                        gcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACAttt                                                                          <  2:1144121/127‑1 (MQ=255)
                                                                        gcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCa                                                              <  1:1446397/139‑1 (MQ=255)
                                                                        gcgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAAGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACAttt                                                                          >  1:1144121/1‑127 (MQ=255)
                                                                         cgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAg                                                             <  2:1195052/139‑1 (MQ=255)
                                                                         cgTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAg                                                             <  1:1533373/139‑1 (MQ=255)
                                                                                          gCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGa                                            >  1:316059/1‑139 (MQ=255)
                                                                                              aCGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTAc                                        <  2:1390576/139‑1 (MQ=255)
                                                                                               cGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGt                                                                                       <  2:276985/91‑1 (MQ=255)
                                                                                               cGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGt                                                                                       >  1:276985/1‑91 (MQ=255)
                                                                                                ggATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTAcgc                                      <  2:448724/139‑1 (MQ=255)
                                                                                                   tGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGc                                   <  1:847388/139‑1 (MQ=255)
                                                                                                   tGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGc                                   <  2:316059/139‑1 (MQ=255)
                                                                                                    ggCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               <  1:513235/110‑1 (MQ=255)
                                                                                                    ggCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               >  2:513235/1‑110 (MQ=255)
                                                                                                    ggCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCt                                  >  1:834786/1‑139 (MQ=255)
                                                                                                     gcgcGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               >  2:1288016/1‑109 (MQ=255)
                                                                                                     gcgcGGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               <  1:1288016/109‑1 (MQ=255)
                                                                                                        cgGGAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCa                              <  1:445793/139‑1 (MQ=255)
                                                                                                           gAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               >  2:263103/1‑103 (MQ=255)
                                                                                                           gAATTTGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               <  1:263103/103‑1 (MQ=255)
                                                                                                                tGTAGGCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCAATGTATCa                      >  2:319580/1‑139 (MQ=255)
                                                                                                                     gCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGt                                                                                            <  1:437372/64‑1 (MQ=255)
                                                                                                                     gCCTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGt                                                                                            >  2:437372/1‑64 (MQ=255)
                                                                                                                      ccTGATAAGACGCGTTAGTGTCGCATCAGGCATCTTCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               <  1:295064/92‑1 (MQ=255)
                                                                                                                      ccTGATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               >  2:295064/1‑92 (MQ=255)
                                                                                                                         gATAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCAATGTATCAGTCGCGAtt             <  2:834786/139‑1 (MQ=255)
                                                                                                                          aTAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTc                                                                                      <  2:1252611/65‑1 (MQ=255)
                                                                                                                          aTAAGACGCGTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTc                                                                                      >  1:1252611/1‑65 (MQ=255)
                                                                                                                                cgcgTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCAATGTATCAGTCGCGATTCACCTg       >  2:511590/1‑138 (MQ=255)
                                                                                                                                cgcgTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCAATGTATCAGTCGCGATTCACCTg       <  1:511590/138‑1 (MQ=255)
                                                                                                                                 gcgTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTgg                                <  2:1188443/112‑1 (MQ=255)
                                                                                                                                 gcgTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTgg                                >  1:1188443/1‑112 (MQ=255)
                                                                                                                                   gTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               >  2:1235952/1‑79 (MQ=255)
                                                                                                                                   gTTAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGc                                                               <  1:1235952/79‑1 (MQ=255)
                                                                                                                                    ttAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGt                                                 <  2:460162/92‑1 (MQ=255)
                                                                                                                                    ttAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGt                                                 >  1:460162/1‑92 (MQ=255)
                                                                                                                                    ttAGTGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCAATGTATCAGTCGCGATTCACCTGCACTc  >  2:1449317/1‑139 (MQ=255)
                                                                                                                                        |                                                                                                                                      
GCGCGAGAATTTGTAGGCCTGATAAGACGCGTTAGCGTCGCATCAGGCATCTGCGCACGACTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGCGCGGGAATTTGTAGGCCTGATAAGACGCGTTAGCGTCGCATCAGGCATCTGCACACGACTGCCGGATGCGATAAACGTCTTGTCCGGCCTACATTTCGCCCGTAGGCAGTCATTAAATAGTTCTGATTACGCGGCTGGCAATGTATCAGTCGCGATTCACCTGCACTC  >  NC_000913/375171‑375441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A