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
A11 F28 I1 R1 228 65.7 2434974 91.7% 2232871 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,417,574 T→C S848P (TCA→CCA)  acrF → multidrug efflux pump RND permease AcrF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,417,5740TC96.1% 167.2 / ‑2.3 51S848P (TCA→CCA) acrFmultidrug efflux pump RND permease AcrF
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (23/26);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

TTACCACTTCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGTCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTTGCTGCACTCT  >  NC_000913/3417440‑3417703
                                                                                                                                      |                                                                                                                                 
ttACCACTTCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCaaaa                                                                                                                              <  1:625743/140‑1 (MQ=255)
  aCCACTTCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAAtt                                                                                                                            >  1:779602/1‑140 (MQ=255)
     aCTTCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTAcc                                                                                                                         <  1:385625/140‑1 (MQ=255)
       ttCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTg                                                                                                                       >  2:895158/1‑140 (MQ=255)
         cacaTTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCg                                                                                                                     >  1:769620/1‑140 (MQ=255)
         cacaTTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCg                                                                                                                     <  2:926468/140‑1 (MQ=255)
           caTTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCggg                                                                                                                   >  1:1096823/1‑140 (MQ=255)
            aTTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGAGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGc                                                                                                                  >  2:476962/1‑140 (MQ=255)
             ttGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCa                                                                                                                 <  1:1122920/140‑1 (MQ=255)
             ttGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCa                                                                                                                 <  1:723269/140‑1 (MQ=255)
               gggTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCAtt                                                                                                               <  1:895158/140‑1 (MQ=255)
                  ggtATGGCTTTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGt                                                                                                            <  2:866018/139‑1 (MQ=255)
                    tATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCg                                                                                                                     <  2:1013316/129‑1 (MQ=255)
                    tATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCg                                                                                                                     >  1:1013316/1‑129 (MQ=255)
                     aTGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTAt                                                                                                         <  1:20559/140‑1 (MQ=255)
                        gCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGAc                                                                                                      >  2:784801/1‑140 (MQ=255)
                         ctctCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACt                                                                                                     >  1:558319/1‑140 (MQ=255)
                          tctcCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGTCAAAATTACCTGCGGGCATTGGTTATGACTg                                                                                                    >  1:442727/1‑140 (MQ=255)
                          tctcCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTg                                                                                                    >  1:741663/1‑140 (MQ=255)
                              cgcgACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTAt                                                                                                         <  2:1217129/131‑1 (MQ=255)
                              cgcgACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTAt                                                                                                         >  1:1217129/1‑131 (MQ=255)
                              cgcgACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACg                                                                                                >  2:912359/1‑140 (MQ=255)
                                 gACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGt                                                                                             <  1:488980/140‑1 (MQ=255)
                                 gACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGt                                                                                             <  2:779602/140‑1 (MQ=255)
                                   cTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTAt                                                                                           >  2:1112029/1‑140 (MQ=255)
                                     ggAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGTCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGt                                                                                         <  2:442727/140‑1 (MQ=255)
                                     ggAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGt                                                                                         <  2:558319/140‑1 (MQ=255)
                                                 cGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAAc                                                                             >  1:1201763/1‑140 (MQ=255)
                                                      tGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTa                                                                        <  1:126638/140‑1 (MQ=255)
                                                                  agaTTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAg                                                            >  2:969364/1‑140 (MQ=255)
                                                                    aTTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGc                                                          <  1:912359/140‑1 (MQ=255)
                                                                       cAGAGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTcc                                                       <  1:476962/140‑1 (MQ=255)
                                                                           gggAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGct                                                   >  1:654472/1‑140 (MQ=255)
                                                                           gggAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGG‑AAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGctc                                                  >  1:683821/1‑140 (MQ=255)
                                                                            ggAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGG‑AAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGctct                                                 <  2:683821/140‑1 (MQ=255)
                                                                              aaGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAAc                                                               <  1:448544/125‑1 (MQ=255)
                                                                              aaGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAAc                                                               >  2:448544/1‑125 (MQ=255)
                                                                                gCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGt                                              <  2:15131/140‑1 (MQ=255)
                                                                                           aaCCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCt                                   <  1:990663/140‑1 (MQ=255)
                                                                                              cAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTtg                                <  1:859994/140‑1 (MQ=255)
                                                                                                 ttCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTgg                             >  1:776059/1‑140 (MQ=255)
                                                                                                            ccATGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCtg                  <  1:784801/140‑1 (MQ=255)
                                                                                                              aTGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCtgtg                <  1:436152/140‑1 (MQ=255)
                                                                                                              aTGGCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCtgtg                <  1:630805/140‑1 (MQ=255)
                                                                                                                ggCGTTGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGcc              <  2:1204751/140‑1 (MQ=255)
                                                                                                                    ttGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTtgc          >  2:21828/1‑140 (MQ=255)
                                                                                                                     tGATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTtgct         <  2:1096823/140‑1 (MQ=255)
                                                                                                                      gATGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTtgctg        >  2:156331/1‑140 (MQ=255)
                                                                                                                       aTGGAAAACCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTtgctgc       >  1:1159408/1‑140 (MQ=255)
                                                                                                                            aaaCCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTTGCTGCActct  >  2:926/1‑140 (MQ=255)
                                                                                                                            aaaCCTTGCGCCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTTGCTGCActct  >  1:154401/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                 
TTACCACTTCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGTCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTTGCTGCACTCT  >  NC_000913/3417440‑3417703

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A