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 2,130,622 T→C 27.9% I95V (ATT→GTT)  mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,130,6220TC27.9% 233.4 / 107.0 154I95V (ATT→GTT) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base T (53/58);  new base C (19/24);  total (72/82)
Fisher's exact test for biased strand distribution p-value = 7.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

Only 100 of 160 total aligned reads displayed.

AAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCG  >  minE/2130552‑2130687
                                                                      |                                                                 
  ggTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                                                 <  1:2725584/71‑1 (MQ=255)
   gtgtGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                                                <  1:1183978/71‑1 (MQ=255)
        aTGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAAt                                                                   >  1:838448/1‑63 (MQ=255)
        aTGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                           >  1:3914307/1‑71 (MQ=255)
           cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                                                 <  1:3606152/62‑1 (MQ=255)
            aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                       <  1:4577236/71‑1 (MQ=255)
            aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                       <  1:2573442/71‑1 (MQ=255)
             tgaTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                                                <  1:4399599/59‑2 (MQ=255)
             tgaTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                                              <  1:2464514/61‑1 (MQ=255)
             gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                                                <  1:2594640/61‑1 (MQ=255)
             gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                                                <  1:126007/61‑1 (MQ=255)
             gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                       >  1:4628389/1‑70 (MQ=255)
               aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                    <  1:4173012/71‑2 (MQ=255)
               aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                    <  1:4250176/71‑2 (MQ=255)
               aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                    <  1:5186317/71‑2 (MQ=255)
               aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                    <  1:1227092/71‑2 (MQ=255)
                tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaa                                                               <  1:1585121/59‑1 (MQ=255)
                tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                                    >  1:2605545/1‑70 (MQ=255)
                 cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaaa                                                              >  1:4121676/1‑59 (MQ=255)
                 cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaaa                                                              >  1:3769785/1‑59 (MQ=255)
                  gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                                                  >  1:1514809/1‑70 (MQ=255)
                  gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                                 >  1:1087905/1‑71 (MQ=255)
                    aCCATTAGCAGAGATATAGGCATAAGTGATGATATAGAGAACGAAGGCAACggt                                                                <  1:2002172/54‑2 (MQ=255)
                        cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                                                  >  1:1605069/1‑64 (MQ=255)
                        cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                               <  1:2089049/67‑1 (MQ=255)
                        cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                               <  1:1466945/67‑1 (MQ=255)
                        cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                             >  1:2427702/1‑69 (MQ=255)
                          agCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGa                                                     <  1:1761793/58‑1 (MQ=255)
                               agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                            >  1:5092420/3‑63 (MQ=255)
                               agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                            >  1:2501159/3‑63 (MQ=255)
                               agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                            >  1:2351582/3‑63 (MQ=255)
                               agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                            >  1:2284749/3‑63 (MQ=255)
                                 atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                                           >  1:3938836/1‑62 (MQ=255)
                                 atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                                           >  1:2791634/1‑62 (MQ=255)
                                 atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                  >  1:1800618/1‑71 (MQ=255)
                                 atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                  <  1:3590723/71‑1 (MQ=255)
                                  tataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGccc                                 <  1:2750719/71‑1 (MQ=255)
                                   ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                                  <  1:5230412/69‑1 (MQ=255)
                                    taGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAg                               >  1:17965/1‑71 (MQ=255)
                                    taGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                                                <  1:1024268/38‑2 (MQ=16)
                                    taGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                                                <  1:503752/38‑2 (MQ=16)
                                    taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                    <  1:1651353/50‑2 (MQ=255)
                                    taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                                                    <  1:652054/50‑2 (MQ=255)
                                    taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                                            >  1:4705894/1‑58 (MQ=255)
                                     aGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                           >  1:2967980/1‑42 (MQ=255)
                                       gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCa                             >  1:2994315/1‑70 (MQ=255)
                                       gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCa                             >  1:3476297/1‑70 (MQ=255)
                                         aTAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                          <  1:5670630/71‑1 (MQ=255)
                                          tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                               <  1:1523296/49‑1 (MQ=255)
                                          tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                         >  1:389185/1‑71 (MQ=255)
                                           aGGTCAGGATATAGAGCACAAAGGCGATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                        >  1:2905092/1‑71 (MQ=255)
                                            ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                             >  1:4955361/1‑49 (MQ=255)
                                            ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                             >  1:2629588/1‑49 (MQ=255)
                                            ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACAACGTTc                                             >  1:5291231/1‑49 (MQ=255)
                                                aGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGt                   >  1:3723559/1‑71 (MQ=255)
                                                 ggATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTg                  <  1:4305190/71‑1 (MQ=255)
                                                  gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                 <  1:2813722/71‑1 (MQ=255)
                                                  gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                 >  1:5392089/1‑71 (MQ=255)
                                                  gATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGa                 >  1:3970433/1‑71 (MQ=255)
                                                    tataGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATg               >  1:1344534/1‑71 (MQ=255)
                                                      taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTg                  >  1:1008746/1‑66 (MQ=255)
                                                      taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                 <  1:3855934/67‑1 (MQ=255)
                                                      taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                 <  1:5029024/67‑1 (MQ=255)
                                                        gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                      <  1:1146724/60‑1 (MQ=255)
                                                        gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                      <  1:1267016/60‑1 (MQ=255)
                                                        gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                      <  1:4053417/60‑1 (MQ=255)
                                                        gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgtg            >  1:836607/1‑70 (MQ=255)
                                                          gCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                    >  1:4798413/1‑60 (MQ=255)
                                                           cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa        <  1:2050087/71‑1 (MQ=255)
                                                           cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa        <  1:3111314/71‑1 (MQ=255)
                                                            acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa        <  1:4131665/67‑1 (MQ=255)
                                                            acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa        <  1:5010047/67‑1 (MQ=255)
                                                            acgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaa        <  1:5535236/67‑1 (MQ=255)
                                                            acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCttt                                     <  1:2357421/41‑1 (MQ=255)
                                                            acaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa        <  1:3226932/70‑1 (MQ=255)
                                                             cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa      >  1:1372428/3‑71 (MQ=255)
                                                             cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa      >  1:190574/3‑71 (MQ=255)
                                                             cgaaGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTaaaa      <  1:223424/69‑1 (MQ=255)
                                                             caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATg               <  1:3569765/62‑1 (MQ=255)
                                                             caAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaaaa      <  1:4942605/71‑1 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                          >  1:3630603/1‑48 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                          >  1:5668755/1‑48 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                         <  1:4152227/49‑1 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                         <  1:1220998/49‑1 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                         <  1:721850/49‑1 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTc   >  1:4489128/1‑71 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTc   <  1:2801628/71‑1 (MQ=255)
                                                                aGGCAATGGAAATGCCGTTAACCACGTTCCAGCCTTTGCCCAGCAAAt                          >  1:2848161/1‑48 (MQ=255)
                                                                aGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTAAAACtg   <  1:3774747/71‑2 (MQ=255)
                                                                aGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTAAAACtg   <  1:2681888/71‑2 (MQ=255)
                                                                 ggCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGGTGTTAAAACtgg  <  1:2852568/71‑3 (MQ=255)
                                                                  gCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                 >  1:4735662/1‑55 (MQ=255)
                                                                  gCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGa                 >  1:3868890/1‑55 (MQ=255)
                                                                    aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                       <  1:3966389/47‑1 (MQ=255)
                                                                    aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                   >  1:940966/1‑51 (MQ=255)
                                                                    aaTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGt                   >  1:5610506/1‑51 (MQ=255)
                                                                     aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                           >  1:5349269/1‑42 (MQ=255)
                                                                     aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                        <  1:4840014/45‑1 (MQ=255)
                                                                     aTGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTgg                    <  1:1938430/49‑1 (MQ=255)
                                                                      tGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                       >  1:644446/1‑45 (MQ=255)
                                                                      |                                                                 
AAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAAAACTCG  >  minE/2130552‑2130687

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