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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,432,994 (C)6→7 coding (567/1125 nt) smf ← DNA recombination‑mediator A family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,432,9881.C100.0% 173.1 / NA 48G191G (GGC→GGG) smfDNA recombination‑mediator A family protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (24/24);  total (24/24)

TGCTGTCACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTAC  >  NC_000913/3432850‑3433110
                                                                                                                                           |                                                                                                                          
tGCTGTCACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAgcg                                                                                                                             <  2:1113488/139‑1 (MQ=255)
         cAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccccctg                                                                                                                   >  1:95609/1‑136 (MQ=255)
                   cTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGa                                                                                                          <  1:642462/139‑1 (MQ=255)
                           aGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGc                                                                                                  >  2:85213/1‑139 (MQ=255)
                             ccGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCa                                                                                                >  1:375116/1‑139 (MQ=255)
                             ccGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCa                                                                                                >  1:124211/1‑139 (MQ=255)
                                cTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTc                                                                                             >  1:90716/1‑139 (MQ=255)
                                             tACCCCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccc                                                                                                                       <  2:255162/99‑1 (MQ=255)
                                             tACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccc                                                                                                                       >  1:255162/1‑99 (MQ=255)
                                                    ttACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccccctg                                                                                                                   >  2:555553/1‑93 (MQ=255)
                                                    ttACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccccctg                                                                                                                   <  1:555553/96‑4 (MQ=255)
                                                     tACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                        <  1:85213/139‑1 (MQ=255)
                                                      aCTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAAt                                                                       <  2:95609/139‑1 (MQ=255)
                                                      aCTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGAGGGGATGAAt                                                                       <  1:496272/139‑1 (MQ=255)
                                                           gACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGt                                                                                              >  1:29347/1‑111 (MQ=255)
                                                           gACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGt                                                                                              <  2:29347/111‑1 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcgg                                                                                  <  2:1052631/122‑1 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcgg                                                                                  >  1:1052631/1‑122 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                        >  2:201786/1‑132 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                        >  2:1298833/1‑132 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                        <  1:201786/132‑1 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                        <  1:1298833/132‑1 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTAtt                                                                 >  1:31534/1‑139 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑cccccc                                                                                                                      >  1:36493/1‑85 (MQ=255)
                                                            aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑cccccc                                                                                                                      <  2:36493/85‑1 (MQ=255)
                                                                cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCgggg                                                                             >  1:229948/1‑123 (MQ=255)
                                                                cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCgggg                                                                             <  2:229948/123‑1 (MQ=255)
                                                                cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGt                                                             >  1:554802/1‑139 (MQ=255)
                                                                cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGt                                                             >  2:1257831/1‑139 (MQ=255)
                                                                cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccc                                                                                                                       >  1:980565/1‑80 (MQ=255)
                                                                cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccc                                                                                                                       <  2:980565/80‑1 (MQ=255)
                                                                 tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc                                                            >  1:1034354/1‑139 (MQ=255)
                                                                 tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc                                                            >  1:533745/1‑139 (MQ=255)
                                                                   aTAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa                                                          <  2:124211/139‑1 (MQ=255)
                                                                   aTAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa                                                          <  2:681337/139‑1 (MQ=255)
                                                                      aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTc                                                       >  1:843549/1‑139 (MQ=255)
                                                                        gCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTccc                                                     <  2:914828/139‑1 (MQ=255)
                                                                        gCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTccc                                                     <  2:554802/139‑1 (MQ=255)
                                                                        gCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTccc                                                     <  2:533745/139‑1 (MQ=255)
                                                                           aTTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccc                                                                                                                       <  1:1013340/69‑1 (MQ=255)
                                                                           aTTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑ccccc                                                                                                                       >  2:1013340/1‑69 (MQ=255)
                                                                             ttcttcGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATa                                                <  2:1034354/139‑1 (MQ=255)
                                                                                 tcGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGc                                            <  2:450414/139‑1 (MQ=255)
                                                                                   gTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAAt                                                                       <  1:154334/110‑1 (MQ=255)
                                                                                   gTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAAt                                                                       >  2:154334/1‑110 (MQ=255)
                                                                                              tAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAg                                                                                               <  2:915484/75‑1 (MQ=255)
                                                                                              tAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAg                                                                                               >  1:915484/1‑75 (MQ=255)
                                                                                                             aCATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCAttt                            <  1:455687/127‑1 (MQ=255)
                                                                                                             aCATCGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCAttt                            >  2:455687/1‑127 (MQ=255)
                                                                                                                 cGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATgga                                                                        >  2:833261/1‑77 (MQ=255)
                                                                                                                 cGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa                                                                        <  1:833261/79‑1 (MQ=255)
                                                                                                                 cGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCtt            >  2:251178/1‑139 (MQ=255)
                                                                                                                 cGAGGGGAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCtt            >  1:201374/1‑139 (MQ=255)
                                                                                                                     gggAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAAACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCttt           >  2:352923/1‑136 (MQ=255)
                                                                                                                     gggAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAAACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCttt           <  1:352923/136‑1 (MQ=255)
                                                                                                                      ggAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTa                     >  2:650249/1‑125 (MQ=255)
                                                                                                                      ggAAATTCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTa                     <  1:650249/125‑1 (MQ=255)
                                                                                                                           ttCCGAGACGAGAGCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTac  <  2:493204/139‑1 (MQ=255)
                                                                                                                                     agagCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCAttt                            <  1:1102464/103‑1 (MQ=255)
                                                                                                                                     agagCGCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCAttt                            >  2:1102464/1‑103 (MQ=255)
                                                                                                                                           |                                                                                                                          
TGCTGTCACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCG‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTAC  >  NC_000913/3432850‑3433110

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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