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 2,584,322 C→T 13.6% L985L (CTG→CTA) ‡ mdtF ← multidrug transporter, RpoS‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,584,3220CT13.6% 250.0 / 22.7 88L985L (CTG→CTA) ‡mdtFmultidrug transporter, RpoS‑dependent
Reads supporting (aligned to +/- strand):  ref base C (38/38);  new base T (5/7);  total (43/45)
Fisher's exact test for biased strand distribution p-value = 7.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01

CCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCG  >  minE/2584254‑2584388
                                                                    |                                                                  
ccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                                  <  1:2775054/71‑1 (MQ=255)
ccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                                  >  1:2239470/1‑71 (MQ=255)
ccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                                  <  1:165949/71‑1 (MQ=255)
ccGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                                  >  1:1901561/1‑71 (MQ=255)
      aTCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                            <  1:606367/71‑1 (MQ=255)
         aCGCCGTTACGTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                            >  1:8647/1‑68 (MQ=255)
         aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                            >  1:1972868/1‑68 (MQ=255)
         aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                            >  1:1453642/1‑68 (MQ=255)
         aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                            >  1:761617/1‑68 (MQ=255)
            ccGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                      <  1:2638641/71‑1 (MQ=255)
             cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                      <  1:389211/70‑1 (MQ=255)
              gatacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATaa                                                    <  1:3682627/69‑1 (MQ=9)
               gTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                     >  1:2777140/1‑69 (MQ=255)
               gTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                     >  1:1324176/1‑69 (MQ=255)
                 acctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                    >  1:548358/1‑68 (MQ=255)
                 acctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                    >  1:1176241/1‑68 (MQ=255)
                   ctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                     <  1:2550853/65‑1 (MQ=255)
                   ctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGc                                                >  1:3605113/1‑70 (MQ=255)
                   ctaccGCGTTTTGCCCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGcc                                               <  1:3879304/71‑1 (MQ=255)
                     accGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcag                                                                  >  1:1470166/1‑50 (MQ=255)
                     acagcgTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGag                                             <  1:3860792/68‑1 (MQ=9)
                      ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGgcagca                                                                >  1:72767/1‑51 (MQ=255)
                      ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCag                                             <  1:78835/70‑1 (MQ=255)
                       cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                           <  1:2617272/71‑1 (MQ=255)
                       cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                              >  1:1033604/1‑68 (MQ=255)
                       cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                              >  1:825207/1‑68 (MQ=255)
                          gTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCAc                                                               >  1:458692/1‑48 (MQ=255)
                          gTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAgg                                        >  1:1638040/1‑71 (MQ=255)
                          gTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAgg                                        >  1:798087/1‑71 (MQ=255)
                             ttGCGCGCCAGAACCGGCACCATGCCTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGCGGtca                                     >  1:683703/1‑71 (MQ=255)
                             ttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAgg                                                 >  1:2058887/1‑59 (MQ=255)
                             ttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAgg                                                 >  1:2755116/1‑59 (MQ=255)
                             ttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCaga                                            >  1:3515077/1‑64 (MQ=255)
                             ctGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtca                                     >  1:3009935/2‑71 (MQ=255)
                              tGCGCGCCAGAACCGGCACCATGAGTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtca                                     <  1:449981/70‑1 (MQ=255)
                               gcgcgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtcat                                    <  1:1818497/70‑1 (MQ=255)
                               gcgcgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtcat                                    <  1:2212633/70‑1 (MQ=255)
                                cgcgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagagag                                         >  1:2061067/1‑64 (MQ=255)
                                  cgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                                <  1:1064270/71‑1 (MQ=255)
                                  cgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAg                                 >  1:778072/1‑70 (MQ=255)
                                  cgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAg                                 <  1:3726042/70‑1 (MQ=255)
                                   gcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                           <  1:3366805/59‑1 (MQ=255)
                                   gcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                           <  1:995071/59‑1 (MQ=255)
                                   gcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                               <  1:2138555/71‑1 (MQ=255)
                                    ccAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAgg                                        <  1:1522864/61‑1 (MQ=255)
                                    ccAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAt                              <  1:2543743/71‑1 (MQ=255)
                                     cAGAACCGGCACCATGACTGATAACCAGCGgcagca                                                                <  1:2425462/36‑1 (MQ=255)
                                     cAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                                   <  1:1447311/49‑1 (MQ=255)
                                      aGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                    >  1:2330768/1‑47 (MQ=255)
                                      aGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTg                            >  1:1199883/1‑71 (MQ=255)
                                      aGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTg                            >  1:2286118/1‑71 (MQ=255)
                                       gAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                           >  1:806792/1‑71 (MQ=255)
                                       gAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                           >  1:2328731/1‑71 (MQ=255)
                                       gAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                           >  1:3322800/1‑71 (MQ=255)
                                        aaCCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTg                            <  1:1525240/69‑1 (MQ=255)
                                         gccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCgagaga                                          >  1:880052/2‑54 (MQ=255)
                                         gccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGAta                             >  1:243958/2‑66 (MQ=12)
                                         aCCGGCACCATGACTGATAACCAGCGGCAGCACGCCga                                                          >  1:2378583/1‑38 (MQ=255)
                                           cGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGt                       <  1:1801768/71‑1 (MQ=255)
                                           cGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGt                       <  1:3420762/71‑1 (MQ=255)
                                            ggCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACgca                      <  1:3777631/71‑3 (MQ=9)
                                            ggCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                      <  1:3368213/71‑1 (MQ=255)
                                             gCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACgca                      >  1:1112377/1‑68 (MQ=9)
                                             gCACCATGACTGATAACCAGCGGCAGCACGCCgaga                                                        >  1:1350824/1‑36 (MQ=255)
                                             gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAtt                             <  1:2733812/63‑1 (MQ=255)
                                             gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaa                     <  1:1463295/71‑1 (MQ=255)
                                             gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaa                     <  1:76557/71‑1 (MQ=255)
                                             gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaa                     <  1:1981888/71‑1 (MQ=255)
                                             gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                      >  1:1854631/1‑70 (MQ=255)
                                             gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                      >  1:1447028/1‑70 (MQ=255)
                                               aCCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAAc                   >  1:3143752/1‑71 (MQ=255)
                                               aCCATGACTGATAACCAGCGGCAGCAAGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaaa                    >  1:478243/1‑70 (MQ=255)
                                                 cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGc                 <  1:3305821/71‑1 (MQ=255)
                                                  aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCa                >  1:1044603/1‑71 (MQ=255)
                                                   ttaCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGgacgcagacgca                >  1:318409/3‑70 (MQ=2)
                                                     aCTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATcc             <  1:2357308/71‑1 (MQ=255)
                                                     aCTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATcc             <  1:2894015/71‑1 (MQ=255)
                                                      cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAggac                         <  1:263185/58‑3 (MQ=9)
                                                      cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAggac                         <  1:3012318/58‑3 (MQ=9)
                                                      cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAggac                         <  1:3151316/58‑3 (MQ=9)
                                                      cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACGCAGACGCAtac             <  1:627934/70‑3 (MQ=9)
                                                      cTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATcc             <  1:35348/70‑1 (MQ=255)
                                                       tGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTgg                           <  1:3715236/55‑1 (MQ=255)
                                                        gATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAtt                             <  1:2947039/52‑1 (MQ=255)
                                                         aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaaa                    >  1:2626189/1‑60 (MQ=255)
                                                         aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCAt               >  1:1428238/1‑65 (MQ=255)
                                                         aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCcgcg          >  1:2795092/1‑70 (MQ=255)
                                                          tAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCgcgc         <  1:634815/70‑1 (MQ=255)
                                                          tAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGcgcc        <  1:264338/71‑1 (MQ=255)
                                                            aCCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGcgccgc      <  1:3082112/71‑1 (MQ=255)
                                                              cAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCtt    <  1:2234995/71‑1 (MQ=255)
                                                               aGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTc   >  1:46695/1‑71 (MQ=255)
                                                                gCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTc   >  1:2027311/1‑70 (MQ=255)
                                                                gCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCg  <  1:3706929/71‑1 (MQ=255)
                                                                 cGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCg  <  1:1936266/70‑1 (MQ=255)
                                                                   gcagcaCGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                               >  1:2192197/1‑39 (MQ=255)
                                                                    cagcaCGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAAc                   <  1:320007/50‑1 (MQ=255)
                                                                    |                                                                  
CCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCG  >  minE/2584254‑2584388

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