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 311,550 A→T 10.5% A441A (GCT→GCA)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,5500AT10.5% 194.4 / 12.9 75A441A (GCT→GCA) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (37/30);  new base T (4/4);  total (41/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

CACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACA  >  minE/311480‑311619
                                                                      |                                                                     
cACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCaga                                                                       <  1:136443/71‑1 (MQ=255)
 aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                                                                      <  1:2957357/71‑1 (MQ=255)
 aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                                                                      <  1:3841463/71‑1 (MQ=255)
   cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCaga                                                                       >  1:2827285/1‑68 (MQ=255)
   cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAACATCGCGATACCGACCAGAgc                                                                     >  1:3517937/1‑70 (MQ=255)
    aGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTgcg                                                                    >  1:3705393/1‑70 (MQ=255)
    aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                                                                   >  1:556739/1‑71 (MQ=255)
     gTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGcc                                                                  >  1:2353725/1‑71 (MQ=255)
        gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                                                                >  1:3370656/1‑70 (MQ=255)
        gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                                                                >  1:3637324/1‑70 (MQ=255)
         aaCCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGa                                                              <  1:3401176/71‑1 (MQ=255)
          aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGaa                                                             >  1:2304363/1‑71 (MQ=255)
            cGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAAtt                                                           <  1:3165198/71‑2 (MQ=255)
             gCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAAttt                                                          >  1:3818268/1‑69 (MQ=255)
             gCCAAAGAAGGCCATCGGTACTAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                                          <  1:3610260/71‑1 (MQ=255)
             gCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                                          <  1:2487857/71‑1 (MQ=255)
               cgaagaatGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGc                                                        >  1:2403519/3‑71 (MQ=255)
               cAAAGAAGGCCATCGGTACGAATACCGCCGACACTACCATCGCGATACCGACCAGAGCGCCCTGa                                                              >  1:2256322/1‑65 (MQ=255)
                aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcc                                                       >  1:403912/1‑71 (MQ=255)
                 aagaagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGccc                                                      >  1:1450726/1‑71 (MQ=255)
                  agaagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTg                                                               >  1:2517569/1‑61 (MQ=255)
                    aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCAt                                                   >  1:3391678/1‑71 (MQ=255)
                      ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGaa                                                             >  1:2542684/1‑59 (MQ=255)
                      ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCg                                                 <  1:2045518/71‑1 (MQ=255)
                        ccATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGat                                               >  1:976105/1‑70 (MQ=255)
                         cATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                                                              <  1:1269278/55‑1 (MQ=255)
                           tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                                          <  1:1606618/57‑1 (MQ=255)
                           tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa                                            >  1:361136/1‑71 (MQ=255)
                            cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                                           >  1:905829/1‑71 (MQ=255)
                            cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                                           >  1:901156/1‑71 (MQ=255)
                             ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                                           <  1:2000163/70‑1 (MQ=255)
                             ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                                           <  1:2640374/70‑1 (MQ=255)
                             ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg                                          >  1:2299603/1‑71 (MQ=255)
                             ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg                                          >  1:3086170/1‑71 (MQ=255)
                               tACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg                                        <  1:1733761/71‑1 (MQ=255)
                                 cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa                                                >  1:709963/1‑61 (MQ=255)
                                 cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg                                        >  1:3645596/1‑69 (MQ=255)
                                 cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGt                                       <  1:611625/70‑1 (MQ=255)
                                  gAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGaa                                                             <  1:1139968/47‑1 (MQ=255)
                                     tACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGctt                                  <  1:1490520/71‑1 (MQ=255)
                                      aCCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGAttttt                                           <  1:3933907/61‑3 (MQ=255)
                                       ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttct                                <  1:3703952/71‑1 (MQ=255)
                                       ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc                                 <  1:1845213/70‑1 (MQ=255)
                                          ccgACAGTACGATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt                                             <  1:2372600/55‑1 (MQ=255)
                                          ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                                          <  1:293599/42‑1 (MQ=255)
                                          ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt                             >  1:3026723/1‑71 (MQ=255)
                                          ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt                             >  1:3561011/1‑71 (MQ=255)
                                          ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt                             >  1:117307/1‑71 (MQ=255)
                                           cgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt                                             <  1:1856760/54‑1 (MQ=255)
                                           cgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTg                            <  1:1364338/71‑1 (MQ=255)
                                            gACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACgg                                         >  1:209257/1‑57 (MQ=255)
                                            gACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTgg                           <  1:161871/71‑1 (MQ=255)
                                                gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcccc                                                     >  1:307287/1‑41 (MQ=255)
                                                gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa                                                <  1:350186/46‑1 (MQ=255)
                                                gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa                                                >  1:1192713/1‑46 (MQ=255)
                                                 tACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggcggc                       >  1:2325397/1‑70 (MQ=255)
                                                 tACCATCGCGATACCGACAAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCa                      <  1:2533555/71‑1 (MQ=255)
                                                 caCCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg                                                 <  1:3603010/43‑1 (MQ=19)
                                                   ccATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggcg                         >  1:411462/1‑66 (MQ=255)
                                                     aTCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAcc                  <  1:1496248/71‑1 (MQ=255)
                                                     aTCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAcc                  >  1:3429363/1‑71 (MQ=255)
                                                      tCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt                             <  1:1957728/59‑1 (MQ=255)
                                                      tCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACct                 >  1:962547/1‑71 (MQ=255)
                                                       ctcgATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACTGGt                                       <  1:3882380/46‑1 (MQ=25)
                                                        gcgATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACctt                <  1:2469835/70‑1 (MQ=255)
                                                          gATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggc                          <  1:2242494/58‑1 (MQ=255)
                                                           aTACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt                                             <  1:3570617/38‑1 (MQ=255)
                                                           aTACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt                                             <  1:2647006/38‑1 (MQ=255)
                                                           aTACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCttcttc            <  1:3357675/71‑1 (MQ=255)
                                                            tACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAc                   >  1:2301690/1‑63 (MQ=255)
                                                            tACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACcttc               <  1:881262/67‑1 (MQ=255)
                                                             aCCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCttt                              >  1:395997/1‑51 (MQ=255)
                                                               cGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGcc        <  1:457362/71‑1 (MQ=255)
                                                                gACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                                           >  1:3423337/1‑35 (MQ=255)
                                                                gACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGctt                                  >  1:1352780/1‑44 (MQ=255)
                                                                 aCCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCa       >  1:1969391/1‑70 (MQ=255)
                                                                  ccAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCAt      >  1:62895/1‑70 (MQ=255)
                                                                   cAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATaa    >  1:3859148/1‑71 (MQ=255)
                                                                   cAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATa     >  1:3353268/1‑70 (MQ=255)
                                                                      agCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGcc        <  1:3562030/64‑1 (MQ=255)
                                                                      agCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAaca  <  1:2813696/70‑1 (MQ=255)
                                                                      |                                                                     
CACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACA  >  minE/311480‑311619

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