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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,634,087 C→T 14.6% L75L (CTC→CTT)  acrD → aminoglycoside/multidrug efflux system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,634,0870CT14.6% 139.7 / 14.8 55L75L (CTC→CTT) acrDaminoglycoside/multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base C (23/23);  new base T (3/5);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 7.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01

GCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCAGGCACC  >  minE/1634022‑1634156
                                                                 |                                                                     
gCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGta                                                                  <  1:2482017/71‑1 (MQ=255)
gCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTAATGta                                                                  <  1:528883/71‑1 (MQ=255)
  ccAGACGCTGGAAACCACCGTGACCCAGGTTATCGCGCAAAATATGACCGGCCTCGATAATCTCAGGtata                                                                >  1:204373/1‑71 (MQ=255)
  ccAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCa                                                                      >  1:3954966/1‑65 (MQ=255)
      aCGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTc                                                            <  1:161985/71‑1 (MQ=255)
       cGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCa                                                           >  1:2274060/1‑71 (MQ=255)
       cGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCa                                                           >  1:2948803/1‑71 (MQ=255)
       cGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCa                                                           >  1:2503643/1‑71 (MQ=255)
            gAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTTATGTATATGTCATCTCa                                                      <  1:3130294/71‑1 (MQ=255)
             aaaaCACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTTATGTATATGTCATCTCag                                                     <  1:1546240/71‑1 (MQ=255)
              aaaCACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTatat                                                               >  1:2252343/1‑60 (MQ=255)
              aaaCACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTatat                                                               >  1:1285510/1‑60 (MQ=255)
              aaaCACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCa                                                      >  1:3311404/1‑69 (MQ=255)
               aaCACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCagag                                                   <  1:1181275/71‑1 (MQ=255)
               aaCACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCagag                                                   <  1:1458802/71‑1 (MQ=255)
               aaCACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCagag                                                   <  1:1761784/71‑1 (MQ=255)
                acacCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTTATGTatat                                                               >  1:2871488/1‑58 (MQ=255)
                          ccAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCa                                                           >  1:1382243/1‑52 (MQ=255)
                            aGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGt                                               >  1:595305/1‑62 (MQ=255)
                            aGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTgg                                             >  1:2958526/1‑64 (MQ=255)
                            aGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGt                                      <  1:3699516/71‑1 (MQ=255)
                             ggTTATCGAGCAAAATATGACCGGCCTCGATAATCTCGTGta                                                                  <  1:225552/42‑1 (MQ=255)
                             ggTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGta                                                                  <  1:1984073/42‑1 (MQ=255)
                             ggTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGt                                      >  1:2900836/1‑70 (MQ=255)
                             gattATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCa                                                      >  1:216393/3‑54 (MQ=255)
                              gTTATCGAGCAAAATATGACCGGCCTCGATAATCTTATGTATATGTCATCTCAGAGCAGTGGCACCGGTCa                                    <  1:1607327/71‑1 (MQ=255)
                              gTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCAtct                                                        <  1:3381182/51‑1 (MQ=255)
                              gTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCAtct                                                        <  1:1030298/51‑1 (MQ=255)
                              gTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCAtct                                                        <  1:2187855/51‑1 (MQ=255)
                               ttATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAg                                   <  1:1701069/71‑1 (MQ=255)
                                tATCGAGCAAAATATGACCGGCCTCGATAATCTTATGTATATGTCAtc                                                         >  1:284302/1‑48 (MQ=255)
                                tATCGAGCAAAATATGACCGGCCTCGATAATCTTATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAgg                                  >  1:3715107/1‑71 (MQ=255)
                                  tCGAGCAAAATATGACCGGCCTCGATAATCTTATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCa                                <  1:772376/71‑1 (MQ=255)
                                      gCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCa                                                 >  1:2370473/1‑50 (MQ=255)
                                        aaaaTATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCg                                        <  1:4075743/57‑1 (MQ=255)
                                        aaaaTATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGt                           <  1:3963719/70‑1 (MQ=255)
                                         aaaTATGACCGGCCTCGATAATCTCATGTATATGTCATCTCa                                                      >  1:486832/1‑42 (MQ=255)
                                          aaTATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCAt                               >  1:654204/1‑64 (MQ=255)
                                          aaTATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCAc                        >  1:1671088/1‑71 (MQ=255)
                                            tatGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCAc                                          >  1:591143/1‑51 (MQ=255)
                                            tatGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCgg                                       >  1:1610411/1‑54 (MQ=255)
                                            tatGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAgga                                 >  1:2231945/1‑59 (MQ=255)
                                              tGACCGGCCTCGATAATCTCATGTATATGTCAtct                                                        <  1:4130363/35‑1 (MQ=255)
                                              tGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTa                    <  1:2564880/71‑1 (MQ=255)
                                                  cGGCCTCGATAATCTCATGTATATGTCATCTCAGAGc                                                  <  1:3126418/37‑1 (MQ=255)
                                                    gCCTCGATAATCTCATTTATATGTCATCTCAGAGc                                                  <  1:520423/35‑1 (MQ=255)
                                                    gCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTa                    <  1:350604/65‑1 (MQ=255)
                                                      cTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCa                         >  1:808989/1‑58 (MQ=255)
                                                      cTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTaa            <  1:203591/71‑1 (MQ=255)
                                                         gATAATCTTATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGt                 <  1:1926354/63‑1 (MQ=255)
                                                         gATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAgg                                  <  1:38375/46‑1 (MQ=255)
                                                         gATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAg          <  1:3375090/70‑1 (MQ=255)
                                                          aTAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCa        <  1:3688995/71‑1 (MQ=255)
                                                            aaTCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAgg                                  >  1:2314523/1‑43 (MQ=255)
                                                             aTCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCAgg      >  1:395182/1‑70 (MQ=255)
                                                               ctcATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCAGGCAc   >  1:134227/1‑71 (MQ=255)
                                                                tcATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCAt                               >  1:2061047/1‑42 (MQ=255)
                                                                tcATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTaa                   >  1:3290275/1‑54 (MQ=255)
                                                                tcATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCAGGCAcc  >  1:2586869/1‑71 (MQ=255)
                                                                 cATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGtt                >  1:1514885/1‑56 (MQ=255)
                                                                 |                                                                     
GCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCAGGCACC  >  minE/1634022‑1634156

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