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
A5 F1 I1 R1 770 51.4 2439994 93.8% 2288714 110.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 852,869 C→T *43* (TAG→TAA)  mntS ← Mn(2)‑response protein, MntR‑repressed

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913852,8690CT100.0% 207.0 / NA 64*43* (TAG→TAA) mntSMn(2)‑response protein, MntR‑repressed
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/34);  total (30/34)

CGTTCAGGTCAACTACTGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGCTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATACACCTCTTGAACTCATTCATAAGA  >  NC_000913/852737‑853001
                                                                                                                                    |                                                                                                                                    
cgTTCAGGTCAACTACTGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTa                                                                                                                                >  1:65706/1‑139 (MQ=255)
   tCAGGTCAACTACTGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCg                                                                                                                             <  2:394522/139‑1 (MQ=255)
   tCAGGTCAACTACTGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCg                                                                                                                             <  1:437581/139‑1 (MQ=255)
            ctactGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTa                                                                                                                    >  1:164096/1‑139 (MQ=255)
            ctactGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTa                                                                                                                    >  2:975639/1‑139 (MQ=255)
               ctGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCt                                                                                                                 >  2:528707/1‑139 (MQ=255)
                     aaCAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTa                                                                                                                    >  2:583245/1‑130 (MQ=255)
                     aaCAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTa                                                                                                                    <  1:583245/130‑1 (MQ=255)
                      aCAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCg                                                                                                          >  1:928777/1‑139 (MQ=255)
                         aaTCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGtt                                                                                                       <  2:164096/139‑1 (MQ=255)
                           tCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTttg                                                                                                     <  1:361746/139‑1 (MQ=255)
                                 gCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCg                                                                                                                             >  2:7369/1‑109 (MQ=255)
                                 gCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCg                                                                                                                             <  1:7369/109‑1 (MQ=255)
                                       gggATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCata                                                                                         <  1:693021/139‑1 (MQ=255)
                                         gATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATc                                                                                       <  2:808889/139‑1 (MQ=255)
                                            tGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    <  2:988154/139‑1 (MQ=255)
                                            tGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    <  1:647507/139‑1 (MQ=255)
                                            tGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    <  1:322205/139‑1 (MQ=255)
                                            tGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTACATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    <  2:13437/139‑1 (MQ=255)
                                             gCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGcac                                                                                   <  1:980361/139‑1 (MQ=255)
                                                 aTCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCacaaca                                                                               >  1:603282/1‑139 (MQ=255)
                                                   ccGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTttgtt                                                                                                   >  1:323291/1‑117 (MQ=255)
                                                   ccGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTttgtt                                                                                                   <  2:323291/117‑1 (MQ=255)
                                                      aCAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGt                                                                                                        >  1:1039049/1‑109 (MQ=255)
                                                      aCAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGt                                                                                                        <  2:1039049/109‑1 (MQ=255)
                                                      aCAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATagag                                                                          >  2:733580/1‑139 (MQ=255)
                                                      aCAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATagag                                                                          >  1:165808/1‑139 (MQ=255)
                                                        aaaaaGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATagagag                                                                        <  1:733580/139‑1 (MQ=255)
                                                              tGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCAt                                                                  <  2:65706/139‑1 (MQ=255)
                                                                     tttCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGt                                                           <  2:194551/139‑1 (MQ=255)
                                                                             cAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTaaa                                                   <  2:93971/139‑1 (MQ=255)
                                                                                              gCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCAtt                                                                 >  2:855943/1‑108 (MQ=255)
                                                                                              gCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCAtt                                                                 <  1:855943/108‑1 (MQ=255)
                                                                                              gCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAaca                                  <  2:512893/139‑1 (MQ=255)
                                                                                               cATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTtgctg                                                                                                            <  1:954532/64‑1 (MQ=255)
                                                                                               cATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTtgctg                                                                                                            >  2:954532/1‑64 (MQ=255)
                                                                                               cATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAacac                                 >  1:1007410/1‑139 (MQ=255)
                                                                                               cATGAAAGCAGGAGTGAAGCGACGTACCGCGACGCCGTTATTTATCGGaa                                                                                                                          <  1:284515/50‑1 (MQ=255)
                                                                                               cATGAAAGCAGGAGTGAAGCGACGTACCGCGACGCCGTTATTTATCGGaa                                                                                                                          >  2:284515/1‑50 (MQ=255)
                                                                                                    aaGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCa                            >  2:165923/1‑139 (MQ=255)
                                                                                                     aGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATa                                                                             <  2:1182618/89‑1 (MQ=255)
                                                                                                     aGCAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATa                                                                             >  1:1182618/1‑89 (MQ=255)
                                                                                                       cAGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATac                         >  1:63995/1‑139 (MQ=255)
                                                                                                        aGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGt                                                           >  2:414980/1‑104 (MQ=255)
                                                                                                        aGGAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGt                                                           <  1:414980/104‑1 (MQ=255)
                                                                                                          gAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    >  2:194260/1‑77 (MQ=255)
                                                                                                          gAGTGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    <  1:194260/77‑1 (MQ=255)
                                                                                                             tGAAGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATACACctct                   >  2:1100299/1‑139 (MQ=255)
                                                                                                               aaGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    >  1:1101236/1‑72 (MQ=255)
                                                                                                               aaGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    <  2:1101236/72‑1 (MQ=255)
                                                                                                                aGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGt                                                           <  1:815101/96‑1 (MQ=255)
                                                                                                                aGCGGCGTACCGCGACGCCGTTATTTATCGGAAGGTTAATCTTTCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGt                                                           >  2:815101/1‑96 (MQ=255)
                                                                                                                    gcgTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATACACCTCTTGAACtc            <  1:1167505/139‑1 (MQ=255)
                                                                                                                     cgTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGtt                                                                                                       >  2:293674/1‑47 (MQ=255)
                                                                                                                     cgTACCGCGACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGtt                                                                                                       <  1:293674/47‑1 (MQ=255)
                                                                                                                          cgcgACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCa                                                                                           >  2:565948/1‑54 (MQ=255)
                                                                                                                          cgcgACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCa                                                                                           <  1:565948/54‑1 (MQ=255)
                                                                                                                          cgcgACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    >  1:257782/1‑61 (MQ=255)
                                                                                                                          cgcgACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGca                                                                                    <  2:257782/61‑1 (MQ=255)
                                                                                                                          cgcgACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTa                                                     >  1:882044/1‑92 (MQ=255)
                                                                                                                          cgcgACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTa                                                     <  2:882044/92‑1 (MQ=255)
                                                                                                                            cgACGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATACACCTCTTGAACTCATTCATaa    <  2:603282/139‑1 (MQ=255)
                                                                                                                              aCGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATACACCTCTTGAACTCATTCATaaaa  >  1:569202/1‑137 (MQ=255)
                                                                                                                              aCGCCGTTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATACACCTCTTGAACTCATTCATAAGa  >  1:149380/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                    
CGTTCAGGTCAACTACTGACGAACAAATCTTTTGCGAAGGGGATTGCAAATCCGACAAAAAGTGGGGTTTTTCAGACCAAAACGCGTTATGCCTGCATGAAAGCAGGAGTGAAGCGGCGTACCGCGACGCCGCTATTTATCGGAAGGTTTATCTTGCTGCGGTTTGTTGTTGACCATATCGCACAACATAGAGAGCAGCATTAACCGTACTTTAAAGGGAGAATGACTAAACACGCGCATACACCTCTTGAACTCATTCATAAGA  >  NC_000913/852737‑853001

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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