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 2,752,776 C→T 24.8% S87S (AGC→AGT)  yhdN → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,752,7760CT24.8% 110.7 / 29.1 88S87S (AGC→AGT) yhdNconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (34/32);  new base T (14/8);  total (48/40)
Fisher's exact test for biased strand distribution p-value = 4.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGTACCGATTTTTTACGCG  >  minE/2752717‑2752840
                                                           |                                                                
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:2632540/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:2413528/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:235993/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:809962/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:2152790/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:1992499/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:1936226/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:3077935/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:1346501/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:1026105/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:541400/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:908513/1‑68 (MQ=255)
cAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGAtt                                                          >  1:1284945/1‑68 (MQ=255)
  gCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGt                                                        <  1:1542146/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:1898/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:2786128/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:2376723/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:1164670/68‑1 (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                                                       <  1:3377406/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:2730092/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:1540781/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:1670909/68‑1 (MQ=255)
   cTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTc                                                       <  1:1661065/68‑1 (MQ=255)
    ttCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCAt                                                     <  1:1319410/69‑1 (MQ=255)
    ttCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCAt                                                     <  1:2704881/69‑1 (MQ=255)
    ttCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCAt                                                     <  1:860202/69‑1 (MQ=255)
           tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                                               <  1:263866/68‑1 (MQ=255)
           tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                                               <  1:720111/68‑1 (MQ=255)
           tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                                               <  1:596420/68‑1 (MQ=255)
           tatTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                                               <  1:3040479/68‑1 (MQ=255)
            atTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTgg                                               <  1:386279/67‑1 (MQ=255)
            atTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGaa                                             >  1:2262013/1‑69 (MQ=255)
                 cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                                         <  1:2664541/68‑1 (MQ=255)
                 cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                                         <  1:1757795/68‑1 (MQ=255)
                 cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                                         <  1:232183/68‑1 (MQ=255)
                 cAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGa                                         <  1:1754042/68‑1 (MQ=255)
                   aaGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCaa                                                     <  1:229921/54‑2 (MQ=255)
                      gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTg                                    >  1:1388585/1‑68 (MQ=255)
                      gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc                                   >  1:261697/1‑69 (MQ=255)
                      gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc                                   >  1:1011867/1‑69 (MQ=255)
                      gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc                                   >  1:3056178/1‑69 (MQ=255)
                      gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc                                   >  1:835746/1‑69 (MQ=255)
                      gTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGc                                   >  1:1532831/1‑69 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGcaca                                >  1:1618647/1‑66 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGc                                   >  1:1419220/1‑66 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:298882/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:3127493/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:603935/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:5630/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:29337/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:677832/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:2903909/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:2870806/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:1084075/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:2200172/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:2135444/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCg                                  >  1:852790/1‑67 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:2930700/69‑1 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:504674/69‑1 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:486732/69‑1 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:1306325/69‑1 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:3319846/69‑1 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:84311/69‑1 (MQ=255)
                         tCCGTCATGATGATCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:1736421/69‑1 (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)
                                  atgatCCGCAATATCAAGAGGTTAGTCGTCGATTGTCATTACTGGAATTGAAGCTGCGAc                                <  1:599835/60‑1 (MQ=255)
                                    gatCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTg                     <  1:573386/69‑1 (MQ=255)
                                    gatCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTg                     <  1:257842/69‑1 (MQ=255)
                                    gatCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTg                     <  1:1434381/69‑1 (MQ=255)
                                       ccGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGt                  >  1:790264/1‑69 (MQ=255)
                                             tatCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTTGATTg                     <  1:1247832/60‑1 (MQ=255)
                                               tCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGTACCGAttt          >  1:2090811/1‑69 (MQ=255)
                                                     ggTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGTACCGATTTTTTAcg    >  1:3173485/1‑69 (MQ=255)
                                                     ggTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGTACCGATTTTTTAcg    >  1:917893/1‑69 (MQ=255)
                                                        tAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGTACCGATTTTTTAcgcg  >  1:313745/1‑68 (MQ=255)
                                                        tAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGTACCGATTTTTTAcgcg  >  1:2917851/1‑68 (MQ=255)
                                                           |                                                                
CAGCTTCTGGATATTCTCAAAGGTATCCGTCACGATGATCCGCAATATCAAGAGGTTAGCCGTCGATTGTCATTACTGGAATTGAAGCTGCGACAAGCTGGATTGAGTACCGATTTTTTACGCG  >  minE/2752717‑2752840

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