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 2,130,596 G→A 9.1% T103T (ACC→ACT)  mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,130,5960GA 9.1% 223.7 / 9.7 78T103T (ACC→ACT) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base G (28/42);  new base A (5/2);  total (33/45)
Fisher's exact test for biased strand distribution p-value = 1.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01

ACGTTTAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTT  >  minE/2130531‑2130666
                                                                 |                                                                      
aCGTTTAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAg                                                                        <  1:1396721/66‑1 (MQ=255)
     tAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGata                                                               >  1:52062/1‑70 (MQ=255)
       gTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGata                                                               >  1:3497767/1‑68 (MQ=255)
         gACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATagag                                                          >  1:2327900/1‑71 (MQ=255)
          aCATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATagag                                                          >  1:238406/1‑70 (MQ=255)
           cATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGca                                                        <  1:829437/71‑1 (MQ=255)
            aTCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGt                                                                      <  1:2843739/56‑1 (MQ=255)
            aTCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGca                                                        >  1:2079159/1‑70 (MQ=255)
                ctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCa                                                                    >  1:2219800/1‑54 (MQ=255)
                 tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                      <  1:3570034/67‑1 (MQ=255)
                 tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                      <  1:1317160/67‑1 (MQ=255)
                 tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                      <  1:2026017/67‑1 (MQ=255)
                    gAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGGCAGGATATaga                                                           <  1:2413942/59‑1 (MQ=255)
                       ggTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATg                                             >  1:2699596/1‑70 (MQ=255)
                        gtgtGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                            >  1:1830348/1‑70 (MQ=255)
                          gtgATTCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCa                                                                    <  1:974314/44‑1 (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)
                            gATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGt                                                                      <  1:1155305/40‑1 (MQ=255)
                            gATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAg                                                                   <  1:901283/43‑1 (MQ=255)
                             aTGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                      >  1:3756300/1‑71 (MQ=255)
                                cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGa                                                                 >  1:1911112/1‑41 (MQ=255)
                                cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACaa                                                     >  1:1656897/1‑53 (MQ=255)
                                cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                    <  1:3419028/70‑1 (MQ=255)
                                cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                    <  1:313305/70‑1 (MQ=255)
                                cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCg                                    <  1:2476653/70‑1 (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                                   <  1:220924/67‑1 (MQ=255)
                                    aTCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGt                                   <  1:2570390/67‑1 (MQ=255)
                                     tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAAt                                              >  1:615111/1‑55 (MQ=255)
                                     tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                               >  1:1333389/1‑70 (MQ=255)
                                     tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                               >  1:2752857/1‑70 (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)
                                         aCCACTGGCAGAAATATAGGCATAGGTCAGtatata                                                             <  1:3513560/36‑1 (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)
                                                                 |                                                                      
ACGTTTAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCTT  >  minE/2130531‑2130666

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