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 454,269 C→G 66.7% T272T (ACG→ACC)  ybgH ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE454,2690CG66.7% 90.6 / 72.1 93T272T (ACG→ACC) ybgHpredicted transporter
Reads supporting (aligned to +/- strand):  ref base C (22/9);  new base G (36/26);  total (58/35)
Fisher's exact test for biased strand distribution p-value = 2.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.79e-01

AAGGCTAATCGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAG  >  minE/454206‑454334
                                                               |                                                                 
aaGGCTAATCGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTcac                                                              >  1:265833/1‑69 (MQ=255)
aaGGCTAATCGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTcac                                                              >  1:2105492/1‑69 (MQ=255)
aaGGCTAATCGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTcac                                                              >  1:720240/1‑69 (MQ=255)
         cGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGc                                                       <  1:1222627/67‑1 (MQ=255)
         cGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGc                                                       <  1:1414855/67‑1 (MQ=255)
         cGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGc                                                       <  1:182124/67‑1 (MQ=255)
            gCTACCCCCCTGTTGTGCGAATGCCCAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCa                                                   <  1:286840/68‑1 (MQ=255)
            gCTACCCCCCTGTTGTGCGAATGCCCAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCa                                                   <  1:3187811/68‑1 (MQ=255)
            gCTACCCCCCTGTTGTGCGAATGCCCAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCa                                                   <  1:3367426/68‑1 (MQ=255)
              tACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCt                                                <  1:1251521/69‑1 (MQ=255)
              tACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCt                                                <  1:1993122/69‑1 (MQ=255)
              tACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCt                                                <  1:811201/69‑1 (MQ=255)
              tACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCt                                                <  1:1581935/69‑1 (MQ=255)
                        ttgtGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTg                                      >  1:1747834/1‑69 (MQ=255)
                        ttgtGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTg                                      >  1:58892/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGtttt                           >  1:2305692/1‑68 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGtttt                           >  1:1790977/1‑68 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:311570/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:11234/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:2266002/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:2382367/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:969270/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:1169824/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:2927921/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:2110715/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:911619/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:395850/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:772244/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:1940833/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:1872910/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTc                          >  1:1662344/1‑69 (MQ=255)
                                    ccAGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTAAGCTGTTTTTGGtttt                           >  1:633953/1‑68 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGtt                             >  1:321731/1‑64 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:3140766/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:89835/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:3020108/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:2989567/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:971492/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:2652927/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:2632299/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:3383827/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:354016/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:1511849/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:2211205/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:166451/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:1724399/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:1947926/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:2022828/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:2050359/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTg                        >  1:2116057/1‑69 (MQ=255)
                                      aGAACAACATGCTGAAGAAGGTGAGGGTAACAATCAGCCCCACCt                                                >  1:236556/1‑45 (MQ=255)
                                         acaacaTACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCtt                     <  1:1179325/69‑1 (MQ=255)
                                         acaacaTACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCtt                     <  1:277675/69‑1 (MQ=255)
                                                 cTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGAGATaa             >  1:574652/1‑69 (MQ=255)
                                                   gaagaaGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGGTTCTGGTTTTCTGCTTTGCGATAAAt           >  1:2918933/1‑69 (MQ=255)
                                                       aagGTGAGGGTAATAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:903632/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTAGGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:3430357/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:3252072/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:1771575/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:3288789/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:1771753/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:176228/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2526161/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:599329/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:1658804/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:1559521/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:795652/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:934281/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:1078636/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:1798430/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2697907/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2736166/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2753931/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2778205/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2815624/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2088730/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2954967/69‑1 (MQ=255)
                                                       aagGTGAGGGTAACAATCAGCCCCAGCTCCTTACGCTGTTTTTGGTTTTCTGCTTTGCGATAAAttttt       <  1:2128877/69‑1 (MQ=255)
                                                         ggTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAAttttt       >  1:2545399/1‑67 (MQ=255)
                                                            gAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:665121/1‑69 (MQ=255)
                                                            gAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:2870460/1‑69 (MQ=255)
                                                            gAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:1725012/1‑69 (MQ=255)
                                                            gAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:848124/1‑69 (MQ=255)
                                                            gAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:1166749/1‑69 (MQ=255)
                                                            gAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:1966800/1‑69 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCGTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCa   >  1:920826/1‑67 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:240434/1‑68 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:213550/1‑68 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:2345067/1‑68 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:128802/1‑68 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:2142653/1‑68 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:2210798/1‑68 (MQ=255)
                                                             aGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAg  >  1:2674125/1‑68 (MQ=255)
                                                               |                                                                 
AAGGCTAATCGAGCTACCGCCCTGTTGTGCGAAGGCCCAGAACAACATACTGAAGAAGGTGAGCGTCACAATCAGCCCCAGCTCCTTCCGCTGTTTCTGGTTTTCTGCTTTGCGATAAATTTTTGCCAG  >  minE/454206‑454334

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