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 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,130,611 C→A 11.6% V98V (GTG→GTT)  mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,130,6110CA11.6% 266.4 / 12.5 86V98V (GTG→GTT) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base C (26/50);  new base A (7/3);  total (33/53)
Fisher's exact test for biased strand distribution p-value = 3.98e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

CATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAA  >  minE/2130542‑2130681
                                                                     |                                                                      
cATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGca                                                                       <  1:829437/71‑1 (MQ=255)
 aTCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGca                                                                       >  1:2079159/1‑70 (MQ=255)
      tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                                     <  1:1317160/67‑1 (MQ=255)
      tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                                     <  1:2026017/67‑1 (MQ=255)
      tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                                     <  1:3570034/67‑1 (MQ=255)
            ggTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATg                                                            >  1:2699596/1‑70 (MQ=255)
             gtgtGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                                           >  1:1830348/1‑70 (MQ=255)
               gtgATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACaa                                                                    <  1:1000448/59‑1 (MQ=255)
                tgATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCaa                                                              >  1:1259575/1‑64 (MQ=255)
                tgATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAAt                                                       >  1:816929/1‑71 (MQ=255)
                tgAAGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCa                                                               >  1:1606479/1‑63 (MQ=255)
                  aTGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                     >  1:3756300/1‑71 (MQ=255)
                     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACaa                                                                    >  1:1656897/1‑53 (MQ=255)
                     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                                   <  1:2476653/70‑1 (MQ=255)
                     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                                   <  1:313305/70‑1 (MQ=255)
                     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                                   <  1:3419028/70‑1 (MQ=255)
                      aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                 >  1:3841630/1‑71 (MQ=255)
                       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                 >  1:3882045/1‑70 (MQ=255)
                       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTg                                                <  1:3419420/71‑1 (MQ=255)
                        aaTCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCa                                                               <  1:2064659/55‑1 (MQ=255)
                        aaTCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCa                                                               <  1:1998809/55‑1 (MQ=255)
                         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGa                                               >  1:2638131/1‑70 (MQ=255)
                         aTCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGt                                                  <  1:2570390/67‑1 (MQ=255)
                         aTCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGt                                                  <  1:220924/67‑1 (MQ=255)
                          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAAt                                                             >  1:615111/1‑55 (MQ=255)
                          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                              >  1:2752857/1‑70 (MQ=255)
                          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                                              >  1:1333389/1‑70 (MQ=255)
                           cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaa                                                         <  1:2238363/58‑1 (MQ=255)
                            gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                           >  1:431476/1‑71 (MQ=255)
                            gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                                           >  1:3038275/1‑71 (MQ=255)
                             caCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAta                                                      >  1:2801671/2‑58 (MQ=255)
                             caCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAta                                                      >  1:578192/2‑58 (MQ=255)
                             aacaacTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                                           <  1:2188696/54‑1 (MQ=255)
                              aCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACgaa                                                                   >  1:3037448/1‑45 (MQ=255)
                              aCCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAAtac                                                     >  1:2706079/1‑57 (MQ=255)
                              aCCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                         <  1:1730270/71‑1 (MQ=255)
                              aCCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                                         <  1:2963379/71‑1 (MQ=255)
                               ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCa                                                               >  1:2968278/1‑48 (MQ=255)
                               ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATg                                                            >  1:3844157/1‑51 (MQ=255)
                               ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                                     >  1:1487521/1‑58 (MQ=255)
                                cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACaaa                                                                   <  1:2793215/43‑1 (MQ=255)
                                cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                 <  1:2286262/61‑1 (MQ=255)
                                cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                 <  1:645678/61‑1 (MQ=255)
                                   tGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAg                                    >  1:1530889/1‑71 (MQ=255)
                                    ggCAGAAATATAGGCATAGGTCAGGATATAGAGCACaa                                                                    <  1:3259477/38‑1 (MQ=255)
                                    ggCAGAAATATAGGCATAGGTCAGGATATAGAGCACaa                                                                    <  1:2447768/38‑1 (MQ=255)
                                     gCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAggt                                  <  1:2258372/71‑3 (MQ=255)
                                      cAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGataa                                            <  1:2207693/60‑4 (MQ=255)
                                      cAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCt                                 <  1:631903/71‑1 (MQ=255)
                                      cAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCt                                 <  1:3900250/71‑1 (MQ=255)
                                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                 <  1:315029/54‑1 (MQ=255)
                                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                                       <  1:1768982/64‑1 (MQ=255)
                                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCtt                                <  1:3786149/71‑1 (MQ=255)
                                       aGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCt                                 <  1:476426/70‑1 (MQ=255)
                                         aaaTATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTg                              <  1:2108386/71‑1 (MQ=255)
                                            tataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc                            <  1:1300912/70‑1 (MQ=255)
                                             ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                                           <  1:1976668/38‑1 (MQ=255)
                                              taGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCa                          <  1:205213/70‑1 (MQ=255)
                                               aGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTg                                                <  1:159205/47‑1 (MQ=255)
                                                ggCATACGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                                 <  1:267439/45‑1 (MQ=255)
                                                 gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaa                      <  1:2968351/71‑1 (MQ=255)
                                                   aTAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGc                        <  1:3927449/67‑1 (MQ=255)
                                                   aTAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt                    <  1:572894/71‑1 (MQ=255)
                                                    tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc                   >  1:79700/1‑71 (MQ=255)
                                                     aGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                  >  1:342043/1‑71 (MQ=255)
                                                     aGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                  >  1:680087/1‑71 (MQ=255)
                                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCtt                 <  1:2775292/71‑1 (MQ=255)
                                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt                  <  1:1548219/70‑1 (MQ=255)
                                                       gTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                <  1:2512851/71‑1 (MQ=255)
                                                       gTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCttt                <  1:2810825/71‑1 (MQ=255)
                                                        tCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTg               <  1:2372374/71‑1 (MQ=255)
                                                          aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                   <  1:2156590/49‑1 (MQ=255)
                                                          aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                   <  1:596894/49‑1 (MQ=255)
                                                          aGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                   <  1:2374901/49‑1 (MQ=255)
                                                           gtatatatAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaaa                     <  1:769920/60‑1 (MQ=255)
                                                            gATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                                   <  1:1485245/47‑1 (MQ=255)
                                                             atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt          >  1:3774950/1‑71 (MQ=255)
                                                             atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt          >  1:1591118/1‑71 (MQ=255)
                                                             atatAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt          <  1:3234720/71‑1 (MQ=255)
                                                              tataGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCaa                      <  1:3151871/58‑1 (MQ=255)
                                                               ataGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATgg        >  1:2353629/1‑71 (MQ=255)
                                                               ataGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATgg        >  1:398382/1‑71 (MQ=255)
                                                                taGAGCACTAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt       <  1:177020/71‑1 (MQ=255)
                                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATgg        <  1:3634079/70‑1 (MQ=255)
                                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt       >  1:1700784/1‑71 (MQ=255)
                                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt       <  1:2526857/71‑1 (MQ=255)
                                                                taGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt       >  1:1037977/1‑71 (MQ=255)
                                                                taGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAGGTGTTACCGATTAAATCTTTGGTGATGgt       <  1:1728274/71‑1 (MQ=255)
                                                                 agagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgt       >  1:378976/1‑70 (MQ=255)
                                                                  gagCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGgtg      <  1:2954836/70‑1 (MQ=255)
                                                                    gCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTc    <  1:2107454/70‑1 (MQ=255)
                                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGAt          <  1:58497/63‑1 (MQ=255)
                                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa  <  1:507759/71‑1 (MQ=255)
                                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa  <  1:3182582/71‑1 (MQ=255)
                                                                     cacaAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCaa  <  1:1773326/71‑1 (MQ=255)
                                                                     |                                                                      
CATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTTTGGTGATGGTGTCAA  >  minE/2130542‑2130681

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