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 309,807 A→T 22.8% V1022V (GTT→GTA)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE309,8070AT22.8% 149.5 / 38.2 70V1022V (GTT→GTA) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (22/32);  new base T (10/6);  total (32/38)
Fisher's exact test for biased strand distribution p-value = 1.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GCTGTGCTCGATATCTTCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGC  >  minE/309744‑309876
                                                               |                                                                     
gCTGTGCTCGATATCTTCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACgaa                                                                  >  1:4735029/1‑69 (MQ=255)
     gCTCGATATCTTCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGAtt                                                           >  1:3632136/1‑71 (MQ=255)
     gCTCGATATCTTCATTCTTGCGGCTAAAGCGGCGGCGAACCACAACAAAGAATACCGGAACgaag                                                                 >  1:5068710/1‑65 (MQ=255)
      cTCGATATCTTCATTCTTGCGGCTATAGCGGCGGCGAACCACCACAAAGAATAGCGGAACgtagaa                                                               <  1:2436516/66‑1 (MQ=38)
             tCTTCATTCTTGCGGCTAAAGCGGCGGCGAACTACCACAAAGAATACCGGAAc                                                                     <  1:3705274/53‑1 (MQ=255)
               ttCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg                                                 >  1:3118460/1‑71 (MQ=255)
                tCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGt                                                >  1:3062001/1‑71 (MQ=255)
                 cATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt                                               >  1:726645/1‑71 (MQ=255)
                  aTTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt                                               <  1:5632875/70‑1 (MQ=255)
                  aTTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt                                               <  1:5639346/70‑1 (MQ=255)
                     cTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGAt                                                            >  1:2279661/1‑54 (MQ=255)
                        gCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGt                                          <  1:1037312/69‑1 (MQ=255)
                        gCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGt                                          <  1:4802089/69‑1 (MQ=255)
                            ttAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt                                    >  1:1446701/2‑71 (MQ=16)
                            ttAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt                                    >  1:221571/2‑71 (MQ=16)
                            cTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg                                                 <  1:5569396/58‑1 (MQ=255)
                             tAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg                                                 <  1:3829365/57‑1 (MQ=255)
                             tAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTg                                              <  1:1550459/60‑1 (MQ=255)
                             tAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt                                    <  1:1254904/70‑1 (MQ=255)
                             tAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt                                    <  1:2154671/70‑1 (MQ=255)
                             tAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt                                    <  1:701302/70‑1 (MQ=255)
                              aaaGCGGCGGCGAACCACCACAAAGAATACCGGAACgaagaa                                                               <  1:611669/42‑1 (MQ=255)
                              aaaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATcc                                  >  1:3255651/1‑71 (MQ=255)
                               aaGCGGCGGCGAACCACCACAAAGAATACCGGAACg                                                                    >  1:3643413/1‑36 (MQ=255)
                               aaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATc                                   <  1:3879147/69‑1 (MQ=255)
                               aaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATc                                   <  1:3234260/69‑1 (MQ=255)
                               aaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATc                                   <  1:2545637/69‑1 (MQ=255)
                                aGCGGCGGCGAACCAACACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCg                                >  1:3422099/1‑71 (MQ=255)
                                  cggcggcgAACCACCACAAAGAATACCGGAACGAAGAAGATT‑CCAGTACCGTTGCGGTCACCATcc                                  >  1:4777737/1‑66 (MQ=255)
                                   ggcggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGcc                              <  1:3265306/70‑1 (MQ=255)
                                   aacggcggATCACCACAAAGAACACCGGTACGAAGAAGATTg                                                          >  1:956319/3‑42 (MQ=18)
                                     cggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGc                                             <  1:4354259/53‑1 (MQ=255)
                                     cggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGc                                             <  1:3891948/53‑1 (MQ=255)
                                     cggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGc                                             <  1:2851986/53‑1 (MQ=255)
                                       gcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTAGCg                                                 <  1:1792654/47‑1 (MQ=255)
                                        cgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa                         <  1:4164197/70‑1 (MQ=255)
                                          aaCCACCACAAAGAATA‑CGGAACGAAGAAGATTGCCAGTAc                                                   >  1:3598405/1‑41 (MQ=38)
                                           accaccACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACAcc                     >  1:4442604/1‑71 (MQ=255)
                                            tcaccacAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTAcccc                     >  1:314986/2‑70 (MQ=255)
                                            ccaccaCAAAGAATACCGGAACGAAGAAGATTGCCAg                                                      <  1:2936979/37‑1 (MQ=255)
                                            ccaccaCAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCa                            >  1:5409611/1‑63 (MQ=255)
                                              accacAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGcc                              <  1:3281504/59‑1 (MQ=255)
                                              accacAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTaccc                      >  1:5354213/1‑65 (MQ=16)
                                                cacaAAGAATACCGGAACGAAGAAGATTGCCAGTAc                                                   >  1:532980/1‑36 (MQ=255)
                                                cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGcc                              <  1:1440765/57‑1 (MQ=255)
                                                cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCa                            >  1:4718558/1‑59 (MQ=255)
                                                cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAc                >  1:4126667/1‑71 (MQ=255)
                                                 acaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACCCCGGTAcc               >  1:5554540/1‑71 (MQ=255)
                                                  caAAGAATACCGGAACTAAGAAGATTGCCAGTACCGTTGCGGTCAc                                       <  1:1065477/46‑1 (MQ=255)
                                                  caAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTTCGGTCAc                                       <  1:4336929/46‑1 (MQ=255)
                                                  caAAGAATACCGGAACCAAGAAGATTGCCAGGACCGTTGCGGCCAc                                       <  1:5163425/46‑1 (MQ=255)
                                                    aaGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa             >  1:5162098/1‑70 (MQ=255)
                                                    aaGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAccca             >  1:849491/1‑68 (MQ=12)
                                                     aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc               <  1:182003/67‑1 (MQ=255)
                                                     aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc               <  1:847248/67‑1 (MQ=255)
                                                     aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc               <  1:625993/67‑1 (MQ=255)
                                                     aGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATtcctcc                              <  1:973145/52‑1 (MQ=12)
                                                     aGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATtcctcc                              <  1:31127/52‑1 (MQ=12)
                                                      gAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCAcag          >  1:2923753/1‑69 (MQ=255)
                                                        acaCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCg        >  1:3298615/3‑71 (MQ=255)
                                                        acaCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCg        >  1:4712527/3‑71 (MQ=255)
                                                         tACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa             >  1:5670355/1‑65 (MQ=255)
                                                         tACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa             >  1:2475731/1‑65 (MQ=255)
                                                          aCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt      <  1:5275557/71‑1 (MQ=255)
                                                           ccGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTac                        <  1:878289/52‑1 (MQ=255)
                                                            cGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAccca             >  1:5372972/1‑60 (MQ=255)
                                                             ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTac                        <  1:5521459/50‑1 (MQ=255)
                                                             ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTg   >  1:309971/1‑71 (MQ=255)
                                                             ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTg   <  1:2365160/71‑1 (MQ=255)
                                                              gAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgc  <  1:2729606/71‑1 (MQ=255)
                                                               aaCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTacac                      >  1:5452146/1‑50 (MQ=255)
                                                               aaCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTacac                      >  1:3542944/1‑50 (MQ=255)
                                                               |                                                                     
GCTGTGCTCGATATCTTCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGC  >  minE/309744‑309876

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A