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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 311,850 A→T 21.2% V341V (GTT→GTA)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,8500AT21.2% 281.4 / 64.0 118V341V (GTT→GTA) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (44/49);  new base T (16/9);  total (60/58)
Fisher's exact test for biased strand distribution p-value = 1.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 132 total aligned reads displayed.

TCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACG  >  minE/311780‑311920
                                                                      |                                                                      
tCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTa                                                                        <  1:3918965/71‑1 (MQ=255)
  gcgcgGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                                                                       >  1:3370189/1‑70 (MQ=255)
  gcgcgGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                                                                       >  1:1197818/1‑70 (MQ=255)
  gcgcgGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAAc                                                                      <  1:2932654/71‑1 (MQ=255)
     cgGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCAc                                                                   <  1:4399059/71‑1 (MQ=255)
          gTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGt                                                              >  1:3065788/1‑71 (MQ=255)
           ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTg                                                             <  1:1266517/71‑1 (MQ=255)
           ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTg                                                             <  1:5126597/71‑1 (MQ=255)
           ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTg                                                             <  1:1448128/71‑1 (MQ=255)
           ttCTGCAAGAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGt                                                              >  1:2819597/1‑70 (MQ=18)
             cTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGaa                                                           >  1:2686001/1‑71 (MQ=255)
                caagAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGaa                                                           >  1:4058890/4‑68 (MQ=21)
                cAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAAt                                                          <  1:207952/69‑1 (MQ=255)
                cAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAAt                                                          <  1:3558846/69‑1 (MQ=255)
                 aGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga                                                       <  1:1660673/71‑1 (MQ=255)
                 aGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga                                                       <  1:836204/71‑1 (MQ=255)
                  agAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATaga                                                       >  1:2064462/2‑70 (MQ=21)
                  agAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATaga                                                       >  1:224138/2‑70 (MQ=21)
                     aCAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATagaaa                                                     >  1:3916900/1‑67 (MQ=18)
                     aCAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCa                                                                    <  1:2979806/54‑1 (MQ=255)
                     aCAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtt                                                   >  1:4570445/1‑71 (MQ=255)
                     aCAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtt                                                   >  1:4664282/1‑71 (MQ=255)
                         aTACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGaa                                                           <  1:1074778/59‑1 (MQ=255)
                         aTACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGaa                                                           <  1:1598976/59‑1 (MQ=255)
                           aCATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCAc                                              >  1:4986943/1‑70 (MQ=255)
                            cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGa                                            <  1:3941275/71‑1 (MQ=255)
                            cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGa                                            <  1:1791893/71‑1 (MQ=255)
                             aTAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCa                                               >  1:4590069/1‑67 (MQ=255)
                             aTAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTACGTGAATAGAGATTTTCa                                               >  1:4825532/1‑67 (MQ=255)
                             aTAACCAGGAACACGAGGATGATCCCTTCGACCAGCGTTTTAACCACTTCGTGaa                                                           >  1:1751603/1‑55 (MQ=255)
                               aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga                                                       >  1:3212469/1‑57 (MQ=255)
                               aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga                                                       >  1:573596/1‑57 (MQ=255)
                               aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga                                                       >  1:5133547/1‑57 (MQ=255)
                               aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga                                                       >  1:1121544/1‑57 (MQ=255)
                               aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga                                                       >  1:3942716/1‑57 (MQ=255)
                                aacAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                                                                       >  1:4258127/3‑40 (MQ=255)
                                aCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                                                                       >  1:4075661/1‑40 (MQ=255)
                                aCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                                                                       >  1:2845680/1‑40 (MQ=255)
                                aCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                                                                       >  1:3716009/1‑40 (MQ=255)
                                  cAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTa                                                                        <  1:4088301/37‑1 (MQ=255)
                                   aGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgt                                     <  1:5323838/71‑1 (MQ=255)
                                    ggAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtg                                    >  1:2177368/1‑71 (MQ=255)
                                    ggAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCgtg                                    >  1:4970918/1‑71 (MQ=255)
                                    ggAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCgtg                                    <  1:3748263/71‑1 (MQ=255)
                                     gAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtttt                                                 <  1:1019905/57‑1 (MQ=255)
                                     gAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAt                                                    >  1:2514016/1‑54 (MQ=255)
                                     gAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATag                                                        <  1:4688178/50‑1 (MQ=255)
                                     gAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCgtgg                                   >  1:4428081/1‑71 (MQ=255)
                                      aaCACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtg                                    >  1:3123258/1‑69 (MQ=255)
                                      aaCACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtg                                    >  1:2557573/1‑69 (MQ=255)
                                      aaCACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtg                                    >  1:4267877/1‑69 (MQ=255)
                                      aaCACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATATTCACGAACGGCgtg                                    >  1:3374507/1‑69 (MQ=255)
                                       acacGAGGATGATCGCTTCGACCAGCGTTTTAACCa                                                                    <  1:4256686/36‑1 (MQ=255)
                                       acacGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtggtg                                 >  1:4649374/1‑71 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGaa                                                           <  1:1091756/42‑1 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtttt                                                 >  1:1144417/1‑52 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTc                                                >  1:4707099/1‑53 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCa                                               >  1:1715554/1‑54 (MQ=255)
                                           gAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCg                              >  1:2362560/1‑70 (MQ=255)
                                            aGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCa                                               >  1:1313830/1‑52 (MQ=255)
                                            aGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGAGTGGTGTCGTa                            >  1:2278972/1‑71 (MQ=255)
                                                tgatCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACg                                         <  1:2902771/54‑1 (MQ=255)
                                                tgatCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgt                                     >  1:4893259/1‑58 (MQ=255)
                                                tgatCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATggg                        >  1:3992616/1‑71 (MQ=255)
                                                  atggCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAggg                        >  1:3219919/4‑69 (MQ=12)
                                                  atggCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAggg                        >  1:3060770/4‑69 (MQ=12)
                                                  atggCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAGGGTa                      <  1:1614961/68‑1 (MQ=16)
                                                  atCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACTGCGTGGTGTCGTATGGGTa                      <  1:2824688/71‑1 (MQ=255)
                                                   tggCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAggg                        >  1:132925/3‑68 (MQ=16)
                                                   tCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGaa                                           >  1:2947451/1‑49 (MQ=255)
                                                     gCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCgtg                                    >  1:614230/1‑54 (MQ=255)
                                                     gCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAGGGTa                      >  1:4444151/1‑68 (MQ=16)
                                                      cTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAAc                   >  1:3778978/1‑70 (MQ=255)
                                                       ttCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACaa                 >  1:3547085/1‑71 (MQ=255)
                                                        tCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAt                >  1:4448835/1‑71 (MQ=255)
                                                        tCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAt                >  1:3574996/1‑71 (MQ=255)
                                                         cGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACaa                 <  1:2911483/69‑1 (MQ=255)
                                                           aCCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAtttt             <  1:286767/71‑1 (MQ=255)
                                                           aCCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAtttt             <  1:4342279/71‑1 (MQ=255)
                                                           aCCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAttt              >  1:5557755/1‑70 (MQ=255)
                                                           aCCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGAAAACAAtttt             <  1:1681204/71‑1 (MQ=255)
                                                             cAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACg                                             <  1:5513063/37‑1 (MQ=255)
                                                             cAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACg                                             <  1:2034661/37‑1 (MQ=255)
                                                             cAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCa           <  1:3497376/71‑1 (MQ=255)
                                                              aGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCg                              <  1:3461784/51‑1 (MQ=255)
                                                               gCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGa         <  1:5143234/71‑1 (MQ=255)
                                                                cGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTa                            >  1:3057517/1‑51 (MQ=255)
                                                                cGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTa                            >  1:2735792/1‑51 (MQ=255)
                                                                  ttttTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTcat                             <  1:4839119/48‑3 (MQ=12)
                                                                  ttttTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTcat                             <  1:4251544/48‑3 (MQ=12)
                                                                  ttttTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTcat                             <  1:1817670/48‑3 (MQ=12)
                                                                  ttttTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATaag                          <  1:2968612/51‑3 (MQ=9)
                                                                  ttttAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAttt              <  1:742067/63‑1 (MQ=255)
                                                                  ttttAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAtt               <  1:3855210/62‑1 (MQ=255)
                                                                    ttAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTAt                           >  1:4541384/1‑48 (MQ=255)
                                                                    ttAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTAt                           >  1:1164868/1‑48 (MQ=255)
                                                                      aaCCACTTCGTGAATAGAGATTTTCACGAACGGCgt                                     <  1:4880805/36‑1 (MQ=255)
                                                                      aaCCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCg                              <  1:668516/43‑1 (MQ=255)
                                                                      aaCCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCg                              <  1:834660/43‑1 (MQ=255)
                                                                      aaCCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACg  >  1:3010050/1‑71 (MQ=255)
                                                                      |                                                                      
TCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACG  >  minE/311780‑311920

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