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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,014,515 C→T 44.1% V518V (GTG→GTA)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,014,5150CT44.1% 26.7 / 78.3 68V518V (GTG→GTA) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base C (19/19);  new base T (16/14);  total (35/33)
Fisher's exact test for biased strand distribution p-value = 8.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01

TGTGAGTTGTATCTGCTGGAAGAAGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATACTTC  >  minE/1014446‑1014585
                                                                     |                                                                      
tgtgAGTTGTATCTGCTGGAAGAAGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTcc                                                                        >  1:5068504/1‑70 (MQ=255)
 gtgAGTTGTATCTGCTGGAAGAAGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCAc                                                                      >  1:4427468/1‑71 (MQ=255)
       tGTATCTGCTGGAAGAAGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAAt                                                                >  1:2839048/1‑71 (MQ=255)
        gTATCTGCTGGAAGAAGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAAt                                                                >  1:565999/1‑70 (MQ=255)
          aTCTGCTGGAAGAAGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAAtttt                                                             >  1:535536/1‑71 (MQ=255)
               ctgGAAGAAGTCGTTACCTTTGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAg                                                         <  1:3389495/70‑1 (MQ=255)
                  gaagaaGTCGTTACCTTTGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGa                                                        >  1:4708865/1‑68 (MQ=255)
                  gaagaaGTCGTTACCTTTGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGAtag                                                     >  1:4840571/1‑69 (MQ=255)
                  gaagaaGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATg                                                      <  1:3396548/70‑1 (MQ=255)
                  gaagaaGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATg                                                      >  1:1281765/1‑70 (MQ=255)
                  caagaagTCGTTACCTTTGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGAtag                                                     >  1:4840576/2‑69 (MQ=255)
                      aagTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTc                                                 >  1:3585077/1‑71 (MQ=255)
                       agTCGTTACCTTTGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTc                                                 <  1:1851522/70‑1 (MQ=255)
                         tCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCAt                                              >  1:1554285/1‑71 (MQ=255)
                          cATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCAtt                                             >  1:3199116/1‑71 (MQ=255)
                           aTTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAAtt                                                               <  1:3480619/52‑1 (MQ=255)
                           aTTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGAt                                                       >  1:5655099/1‑60 (MQ=255)
                            tttCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTcc                                           >  1:489388/1‑71 (MQ=255)
                             taccTTTGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTc                                                            <  1:384221/51‑1 (MQ=25)
                                cTTTGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTcga                                                                 <  1:4102925/45‑3 (MQ=21)
                                 tttGTCATCGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCAt                                              <  1:5383765/63‑1 (MQ=255)
                                  ttgtcatcGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAGCTc                                     >  1:1254032/4‑71 (MQ=255)
                                   tgtcatcGACCAGGATAAACGCCGGGAAATCTTCTACTTCGAtttt                                                             >  1:1219716/3‑46 (MQ=21)
                                   tgtcatcGACCAGGATAAACGCCGGGAAATCTTCTACTTCGAtttt                                                             >  1:2888147/3‑46 (MQ=21)
                                       atcGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAGCTCCGGa                                 >  1:5086069/1‑70 (MQ=255)
                                       atcGACCAGGATAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAGCTCCGGa                                 >  1:2639127/1‑70 (MQ=255)
                                        tcCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTcc                                                           <  1:3869038/43‑1 (MQ=255)
                                        tcCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTcc                                                           <  1:2663123/43‑1 (MQ=255)
                                         ccACAAGGATAAACGCCGGGAAATCTTCCACTTCaa                                                                 <  1:995606/36‑1 (MQ=255)
                                         ccACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTccc                                          >  1:2747386/1‑59 (MQ=255)
                                          cacaAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGatat                              >  1:1079912/1‑70 (MQ=255)
                                          cacaAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGatat                              >  1:1175426/1‑70 (MQ=255)
                                          cacaAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATAtt                             >  1:453674/1‑71 (MQ=255)
                                           acaAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTcc                                           <  1:2981343/56‑1 (MQ=255)
                                            caAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGa                                                        <  1:1626221/42‑1 (MQ=255)
                                             aaGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTc                            >  1:5501114/1‑69 (MQ=255)
                                              aGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGa                                                        <  1:3495772/40‑1 (MQ=255)
                                              aGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCa                                               >  1:1172567/1‑49 (MQ=255)
                                                  tAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCtt                                                  <  1:4758803/42‑1 (MQ=255)
                                                  tAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCa                                         >  1:119644/1‑51 (MQ=255)
                                                  tAAACGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCa                                         >  1:126505/1‑51 (MQ=255)
                                                  tAAACGCCGGGAAATCTTCTACTTCGATTTTCAAGATAGCTTCCATACCCAGCTCCGGa                                 >  1:275311/1‑59 (MQ=255)
                                                  tAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCg                                   <  1:1877283/57‑1 (MQ=255)
                                                  tAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACAt                     >  1:2076490/1‑71 (MQ=255)
                                                    aaCGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCaa                          <  1:10312/64‑1 (MQ=255)
                                                     aCGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCa                                               >  1:1908448/1‑42 (MQ=255)
                                                     aCGCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATAcc                                           >  1:4521493/1‑46 (MQ=255)
                                                      cGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCa                 <  1:358922/71‑1 (MQ=255)
                                                      cGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCa                 <  1:4026277/71‑1 (MQ=255)
                                                      cGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCa                 <  1:4032262/71‑1 (MQ=255)
                                                       gCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCtt                                                  <  1:4636530/37‑1 (MQ=37)
                                                       gCCGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAg                                        >  1:4561960/1‑47 (MQ=255)
                                                         cGGGAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAGCTCCGGATAAGCGACGCACTCCAgat              <  1:1093234/71‑3 (MQ=255)
                                                         cGGGAAATCTTCTACTTCGATTTTCCAGATAGATTcc                                                >  1:1111159/1‑37 (MQ=25)
                                                          gggAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGct             <  1:2595090/71‑1 (MQ=255)
                                                           ggAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAgc                                       <  1:450747/44‑2 (MQ=255)
                                                           ggAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAgc                                       <  1:3154114/44‑2 (MQ=255)
                                                           ggAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAgc                                       <  1:878322/44‑2 (MQ=255)
                                                           ggAAATCTTCTACTTCGATTTTCCAGATAGCTTCCATACCCAGCTCCg                                   <  1:3488393/48‑1 (MQ=255)
                                                           ggAAATCTTCTACTTCGATTTTCCAGATAGATTCCATACCCAGCTCCGGATAAGCGACGCACTCCAgatg             >  1:5477308/1‑67 (MQ=255)
                                                             aaaTCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTc                                     <  1:4764458/44‑1 (MQ=255)
                                                             aaaTCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTc                                     <  1:1354722/44‑1 (MQ=255)
                                                             aaaTCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCtt          <  1:1585056/71‑1 (MQ=255)
                                                                 cTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATa      >  1:5071271/1‑71 (MQ=255)
                                                                  ttCTACTTCGATTTTCCAGATAGCTTCCATACCCAGCTcc                                    <  1:4732056/40‑1 (MQ=255)
                                                                  ttCTACTTCGATTTTCCAGATAGCTTCCATACCCAGCTcc                                    <  1:2219373/40‑1 (MQ=255)
                                                                  ttCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTc                            <  1:351022/48‑1 (MQ=255)
                                                                  ttCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTc                            <  1:1886663/48‑1 (MQ=255)
                                                                  ttCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATa      >  1:3467154/1‑70 (MQ=255)
                                                                     cACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAgg               >  1:5163477/1‑58 (MQ=255)
                                                                     cACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATa      >  1:388147/1‑67 (MQ=255)
                                                                     cACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATa      >  1:3412052/1‑67 (MQ=255)
                                                                     cACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATACtt   <  1:4335428/70‑1 (MQ=255)
                                                                     cACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATAATCAACACATTCCAGGCTCTTAATACtt   <  1:2827364/70‑1 (MQ=255)
                                                                     cACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCAGGATATTCAACACATTCCAgg               >  1:3877106/1‑58 (MQ=255)
                                                                     cACTTCAATTTTCCAGATGGCTTCCACTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATACTTc  >  1:5353610/1‑71 (MQ=255)
                                                                     |                                                                      
TGTGAGTTGTATCTGCTGGAAGAAGTCATTTCCTTTATCATCCACAAGGATAAACGCCGGGAAATCTTCCACTTCAATTTTCCAGATGGCTTCCATTCCCAGTTCCGGATATTCAACACATTCCAGGCTCTTAATACTTC  >  minE/1014446‑1014585

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A