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 1,621,531 T→C 60.9% V65V (GTA→GTG)  eutP ← conserved hypothetical protein with nucleoside triphosphate hydrolase domain

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,621,5310TC60.9% 53.7 / 67.2 103V65V (GTA→GTG) eutPconserved hypothetical protein with nucleoside triphosphate hydrolase domain
Reads supporting (aligned to +/- strand):  ref base T (25/15);  new base C (23/39);  total (49/54)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.78e-01

Only 100 of 104 total aligned reads displayed.

TCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTAAAATATTCACCCGGCGTATC  >  minE/1621466‑1621599
                                                                 |                                                                    
tCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTAc                                                                    >  1:1843862/1‑68 (MQ=255)
tCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACa                                                                   >  1:2013254/1‑69 (MQ=255)
tCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACa                                                                   >  1:1648880/1‑69 (MQ=255)
tCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACa                                                                   >  1:2613206/1‑69 (MQ=255)
tCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACa                                                                   >  1:2017102/1‑69 (MQ=255)
tCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACa                                                                   >  1:743738/1‑69 (MQ=255)
tCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACa                                                                   >  1:2214968/1‑69 (MQ=255)
tCCAGCAACCCGGCAGGCAACCGACCTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGGCTACa                                                                   <  1:3153433/69‑1 (MQ=255)
  cAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATc                                                                 >  1:78791/1‑69 (MQ=255)
  cAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATc                                                                 >  1:1950123/1‑69 (MQ=255)
      aaCCCGGCAGGCAACCGACTTTCCGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGt                                                             <  1:2191481/69‑1 (MQ=255)
      aaCCCGGCAGGCAACCGACTTTCCGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGt                                                             <  1:2804032/69‑1 (MQ=255)
      aaCCCGGCAGGCAACCGACTTTCCGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGt                                                             <  1:2950222/69‑1 (MQ=255)
      aaCCCGGCAGGCAACCGACTTTCCGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGt                                                             <  1:2953380/69‑1 (MQ=255)
      aaCCCGGCAGGCAACCGACTTTCCGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGt                                                             <  1:2312397/69‑1 (MQ=255)
      aaCCCGGCAGGCAACCGACTTTCCGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGt                                                             <  1:1038250/69‑1 (MQ=255)
              aggcaACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGt                                                     <  1:3201534/69‑1 (MQ=255)
              aggcaACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGt                                                     <  1:1949214/69‑1 (MQ=255)
              aggcaACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGt                                                     <  1:2131052/69‑1 (MQ=255)
              aggcaACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGt                                                     <  1:2885341/69‑1 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGc                                                          >  1:788297/1‑61 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTaa                                                   >  1:1261011/1‑68 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTaa                                                   >  1:2143365/1‑68 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTaa                                                   >  1:1578273/1‑68 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTaa                                                   >  1:809540/1‑68 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTaa                                                   >  1:311719/1‑68 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTaa                                                   >  1:1362057/1‑68 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTa                                                    >  1:1787695/1‑67 (MQ=255)
                 caACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTa                                                    >  1:679419/1‑67 (MQ=255)
                   aCCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTa                                                <  1:2175282/69‑1 (MQ=255)
                   aCCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTa                                                <  1:2079677/69‑1 (MQ=255)
                   aCCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTa                                                <  1:1599147/69‑1 (MQ=255)
                   aCCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTa                                                <  1:438972/69‑1 (MQ=255)
                   aCCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTa                                                <  1:1331760/69‑1 (MQ=255)
                   aCCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTa                                                <  1:799202/69‑1 (MQ=255)
                          tgccGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGt                                          <  1:3378674/66‑1 (MQ=255)
                          tgccGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGt                                          <  1:1985386/66‑1 (MQ=255)
                          tgccGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGt                                          <  1:383097/66‑1 (MQ=255)
                          tgccGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGt                                          <  1:392808/66‑1 (MQ=255)
                          tgccGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGt                                          <  1:646249/66‑1 (MQ=255)
                           gccGGGTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGt                                          <  1:2965682/66‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:2811337/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:361945/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:427400/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:922272/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:2272000/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:218866/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:1492837/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:1986/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:1344336/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:1787442/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:1351422/69‑1 (MQ=255)
                               ggTCATTCGCGCCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATAcc                                    <  1:1936064/69‑1 (MQ=255)
                                       gcgcCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTa                                                <  1:462121/49‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:1539452/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:1549990/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:1534598/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:491088/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:2985101/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:527687/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:562852/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:2720596/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:1329663/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:252682/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:2505341/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:2132364/46‑1 (MQ=255)
                                         gcCGTGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:838163/46‑1 (MQ=255)
                                         gcCATGGACATAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:1535743/46‑1 (MQ=255)
                                               gACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTaa                     >  1:1985159/1‑68 (MQ=255)
                                                  aTAGATCAGCATGTCCACATCCTGTAGCGTGGTAAtt                                                 <  1:1347077/37‑1 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:703338/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:671696/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:531517/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1161577/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1088177/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1078472/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1645772/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:3396471/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:2200007/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:2056273/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:253071/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:2630872/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:2645988/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:2696179/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:2744468/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1767775/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:3018625/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:3057597/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:3101487/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1679623/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1612288/1‑54 (MQ=255)
                                                    aGATCAGCATGTCCACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1544301/1‑54 (MQ=255)
                                                    aGATCAGCATGTCAACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCggg                              >  1:1377045/1‑54 (MQ=255)
                                                     gATCAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTAAAATATTc              >  1:1687913/1‑69 (MQ=255)
                                                     gATCAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTAAAATATTc              >  1:2875835/1‑69 (MQ=255)
                                                     gATCAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTAAAATATTc              >  1:1826064/1‑69 (MQ=255)
                                                     gATCAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTAAAATATTc              >  1:502524/1‑69 (MQ=255)
                                                        cAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGAt                           <  1:562835/53‑1 (MQ=255)
                                                        cAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGAt                           <  1:2170178/53‑1 (MQ=255)
                                                                 tACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTAAAATATTCACCCGGCGTATc  <  1:1739630/69‑1 (MQ=255)
                                                                 |                                                                    
TCCAGCAACCCGGCAGGCAACCGACTTTCCGGGTCATTTGCGCCATGGACATAGATCAGCATGTCTACATCCTGTAGCGTGGTAATTAAGGCGTGATACCAGCGGGGATGGTTAAAATATTCACCCGGCGTATC  >  minE/1621466‑1621599

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A