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 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 775,538 A→G 6.9% K387K (AAA→AAG)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE775,5380AG 6.9% 255.2 / 8.3 88K387K (AAA→AAG) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base A (42/39);  new base G (2/4);  total (44/44)
Fisher's exact test for biased strand distribution p-value = 4.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACG  >  minE/775469‑775608
                                                                     |                                                                      
gcgcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGaaaa                                                                       >  1:2760384/1‑71 (MQ=255)
 cgcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGaaaa                                                                       <  1:1102444/70‑1 (MQ=255)
 cgcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGaaaa                                                                       <  1:252022/70‑1 (MQ=255)
  gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                                                                     <  1:1646411/71‑1 (MQ=255)
  gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                                                                     <  1:641765/71‑1 (MQ=255)
      caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa                                                                 >  1:2962525/1‑71 (MQ=255)
       aTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                >  1:2254841/1‑71 (MQ=255)
          ggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                                                              <  1:1580269/70‑1 (MQ=255)
                aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACtt                                                       >  1:2124198/1‑71 (MQ=255)
                aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACtt                                                       >  1:2989566/1‑71 (MQ=255)
                 ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                      <  1:735793/71‑1 (MQ=255)
                 ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                      <  1:147683/71‑1 (MQ=255)
                 ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                      <  1:358606/71‑1 (MQ=255)
                 ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                      <  1:799059/71‑1 (MQ=255)
                  cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                >  1:2371678/1‑60 (MQ=255)
                  cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                >  1:136292/1‑60 (MQ=255)
                  cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                >  1:1654174/1‑60 (MQ=255)
                  cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                      <  1:2343621/70‑1 (MQ=255)
                   gAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                      >  1:1316175/1‑69 (MQ=255)
                   gAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa                                                    <  1:299497/71‑1 (MQ=255)
                    aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                   >  1:2997238/1‑71 (MQ=255)
                         gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg                                                   >  1:3392326/1‑66 (MQ=255)
                          cTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                              <  1:2268823/70‑1 (MQ=255)
                           tGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGt                                                                   <  1:2037227/48‑1 (MQ=255)
                           tGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGt                                                                   <  1:2888927/48‑1 (MQ=255)
                           tGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGt                                                                   <  1:2579026/48‑1 (MQ=255)
                           tGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGt                                                                   <  1:3251941/48‑1 (MQ=255)
                           tGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGt                                                                   <  1:732190/48‑1 (MQ=255)
                              cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc                                                  <  1:299933/62‑1 (MQ=255)
                              cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                          >  1:1841684/1‑70 (MQ=255)
                              cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                          >  1:2564693/1‑70 (MQ=255)
                              cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                          >  1:383624/1‑70 (MQ=255)
                              cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTga                                            >  1:729976/1‑68 (MQ=255)
                              cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTga                                            >  1:111326/1‑68 (MQ=255)
                              cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTga                                            >  1:2883717/1‑68 (MQ=255)
                               ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                              <  1:3462876/65‑1 (MQ=255)
                               ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                              <  1:2872751/65‑1 (MQ=255)
                                tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                       >  1:2905505/1‑71 (MQ=255)
                                tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                       >  1:2401662/1‑71 (MQ=255)
                                tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                       >  1:97970/1‑71 (MQ=255)
                                 aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg                                      >  1:3383743/1‑71 (MQ=255)
                                       tAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                              >  1:3363553/1‑57 (MQ=255)
                                       tAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                              >  1:2685110/1‑57 (MQ=255)
                                          aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                       >  1:3037691/1‑61 (MQ=255)
                                          aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                             >  1:2725117/1‑71 (MQ=255)
                                          aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                             >  1:2653645/1‑71 (MQ=255)
                                          aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                             >  1:2162471/1‑71 (MQ=255)
                                           ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                          <  1:455388/57‑1 (MQ=255)
                                           ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                          <  1:389699/57‑1 (MQ=255)
                                           ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg                                          <  1:2406373/57‑1 (MQ=255)
                                           ggTATGGAAGGCGCAATCAACGCGAAAACCGCAACCTATGACTTCGAGCGTCTgatg                                          <  1:810680/57‑1 (MQ=255)
                                            gTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGctg                           <  1:2020763/71‑1 (MQ=255)
                                              aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                         >  1:462304/1‑71 (MQ=255)
                                              aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                         >  1:257647/1‑71 (MQ=255)
                                              aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                         >  1:1981864/1‑71 (MQ=255)
                                              aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                         >  1:947763/1‑71 (MQ=255)
                                              aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                         >  1:3227925/1‑71 (MQ=255)
                                                ggAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                         <  1:1197818/69‑1 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt                                                        >  1:2346304/1‑37 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt                                                        >  1:2315324/1‑37 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt                                                        >  1:1256360/1‑37 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt                                                        >  1:3463852/1‑37 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt                                                        >  1:926072/1‑37 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                     <  1:865985/56‑1 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                     <  1:850966/56‑1 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                       <  1:2949979/70‑1 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                       <  1:565330/70‑1 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                       <  1:1088655/70‑1 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                       <  1:27788/70‑1 (MQ=255)
                                                 gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa                       <  1:1786808/70‑1 (MQ=255)
                                                   aGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAt                    <  1:3096395/71‑1 (MQ=255)
                                                     gcgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGt                  <  1:1772844/71‑1 (MQ=255)
                                                     gcgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGt                  <  1:831941/71‑1 (MQ=255)
                                                      cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGt                                                >  1:2298059/1‑40 (MQ=255)
                                                      cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                     >  1:1141043/1‑51 (MQ=255)
                                                       gcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGt                  <  1:1983688/69‑1 (MQ=255)
                                                       gcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGt                  <  1:3233730/69‑1 (MQ=255)
                                                       gcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGt                  <  1:1362592/69‑1 (MQ=255)
                                                       gcAATCAACGCGAATACCGTAACCTATGACTTCGAGc                                                  <  1:1598405/37‑1 (MQ=255)
                                                         aaTCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGt                  <  1:1612837/67‑1 (MQ=255)
                                                           tCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                       >  1:3710811/1‑60 (MQ=25)
                                                           tCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa                       >  1:1675238/1‑60 (MQ=25)
                                                           tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa               <  1:2149317/68‑1 (MQ=255)
                                                           tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa               <  1:1345910/68‑1 (MQ=255)
                                                           tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa               <  1:3367238/68‑1 (MQ=255)
                                                             aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                       >  1:833945/1‑42 (MQ=255)
                                                             aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                       >  1:2577245/1‑42 (MQ=255)
                                                             aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt          >  1:1676387/1‑71 (MQ=255)
                                                             aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt          >  1:1790612/1‑71 (MQ=255)
                                                               cgcgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTg        <  1:707240/71‑1 (MQ=255)
                                                               cgcgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTg        <  1:3490477/71‑1 (MQ=255)
                                                                   aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGATAAACTGCTGAAATGTTCAGAGTTTGGTg     <  1:1192230/70‑1 (MQ=255)
                                                                     aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcg  >  1:1701850/1‑71 (MQ=255)
                                                                     aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcg  >  1:2773391/1‑71 (MQ=255)
                                                                     aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcg  >  1:998428/1‑71 (MQ=255)
                                                                     |                                                                      
GCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACG  >  minE/775469‑775608

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