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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,752,749 C→T 23.7% H78H (CAC→CAT)  yhdN → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,752,7490CT23.7% 116.7 / 27.5 88H78H (CAC→CAT) yhdNconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (30/37);  new base T (14/7);  total (44/44)
Fisher's exact test for biased strand distribution p-value = 1.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTG  >  minE/2752681‑2752816
                                                                    |                                                                   
ttACCGCCAGAACTT‑AGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:1429856/68‑1 (MQ=255)
 tACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:2900485/68‑1 (MQ=255)
 tACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:1697686/68‑1 (MQ=255)
 tACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:1434404/68‑1 (MQ=255)
 tACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:2057818/68‑1 (MQ=255)
 tACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:717787/68‑1 (MQ=255)
 tACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:923824/68‑1 (MQ=255)
 tACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCAc                                                                     <  1:1296818/68‑1 (MQ=255)
     gCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACgatg                                                                 <  1:2268912/68‑1 (MQ=255)
     gCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACgatg                                                                 <  1:3002091/68‑1 (MQ=255)
     gCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACgatg                                                                 <  1:1077669/68‑1 (MQ=255)
     gCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACgatg                                                                 <  1:2354495/68‑1 (MQ=255)
     gCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACgatg                                                                 <  1:165909/68‑1 (MQ=255)
          aaCTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGc                                                           >  1:872255/1‑69 (MQ=255)
          aaCTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGc                                                           >  1:163144/1‑69 (MQ=255)
                              gCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACg                                                                    <  1:2754164/40‑1 (MQ=255)
                              gCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACg                                                                    <  1:1742381/40‑1 (MQ=255)
                              gCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACg                                                                    <  1:656263/40‑1 (MQ=255)
                              gCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACg                                                                    <  1:2717862/40‑1 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:908513/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:2413528/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:235993/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:541400/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:3077935/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:1936226/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:1992499/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:2632540/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:1026105/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:809962/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:1346501/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:1284945/1‑68 (MQ=255)
                                    cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                  >  1:2152790/1‑68 (MQ=255)
                                      gCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGt                                <  1:1542146/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:2376723/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:1898/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:2730092/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:2786128/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:2149877/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:2140919/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:2121923/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:2065232/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:1164670/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:1540781/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:3377406/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:1661065/68‑1 (MQ=255)
                                       cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                               <  1:1670909/68‑1 (MQ=255)
                                        ttCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCAt                             <  1:860202/69‑1 (MQ=255)
                                        ttCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCAt                             <  1:1319410/69‑1 (MQ=255)
                                        ttCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCAt                             <  1:2704881/69‑1 (MQ=255)
                                               tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                       <  1:3040479/68‑1 (MQ=255)
                                               tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                       <  1:263866/68‑1 (MQ=255)
                                               tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                       <  1:596420/68‑1 (MQ=255)
                                               tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                       <  1:720111/68‑1 (MQ=255)
                                                atTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                       <  1:386279/67‑1 (MQ=255)
                                                atTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGaa                     >  1:2262013/1‑69 (MQ=255)
                                                     cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                 <  1:1754042/68‑1 (MQ=255)
                                                     cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                 <  1:232183/68‑1 (MQ=255)
                                                     cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                 <  1:2664541/68‑1 (MQ=255)
                                                     cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                 <  1:1757795/68‑1 (MQ=255)
                                                       aaGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCaa                             <  1:229921/54‑2 (MQ=255)
                                                          gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTg            >  1:1388585/1‑68 (MQ=255)
                                                          gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc           >  1:3056178/1‑69 (MQ=255)
                                                          gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc           >  1:1011867/1‑69 (MQ=255)
                                                          gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc           >  1:835746/1‑69 (MQ=255)
                                                          gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc           >  1:1532831/1‑69 (MQ=255)
                                                          gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc           >  1:261697/1‑69 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGcaca        >  1:1618647/1‑66 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGc           >  1:1419220/1‑66 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:1084075/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:603935/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:5630/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:2903909/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:677832/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:2135444/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:3127493/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:2200172/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:2870806/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:298882/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:29337/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg          >  1:852790/1‑67 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc        <  1:504674/69‑1 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc        <  1:1306325/69‑1 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc        <  1:84311/69‑1 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc        <  1:486732/69‑1 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc        <  1:1736421/69‑1 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc        <  1:3319846/69‑1 (MQ=255)
                                                             tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc        <  1:2930700/69‑1 (MQ=255)
                                                               cGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACaa      <  1:1350664/69‑1 (MQ=255)
                                                                  cACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGc    >  1:2485582/1‑68 (MQ=255)
                                                                   aCGATGATCCTCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTg  >  1:1688017/1‑69 (MQ=255)
                                                                   aCGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTg  >  1:976530/1‑69 (MQ=255)
                                                                   aCGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTg  >  1:558105/1‑69 (MQ=255)
                                                                   aCGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTg  >  1:234329/1‑69 (MQ=255)
                                                                   aCGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTg  >  1:166181/1‑69 (MQ=255)
                                                                   aCGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTg  >  1:1331367/1‑69 (MQ=255)
                                                                   aCGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTg  >  1:1022163/1‑69 (MQ=255)
                                                                    |                                                                   
TTACCGCCAGAACTTGAGCAACGGAGAGAAGCAATTCAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTG  >  minE/2752681‑2752816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A