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
A2 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,540,373 G→T 24.9% D300Y (GAT→TAT)  rfaJ → UDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,540,3730GT24.9% 254.0 / 49.5 100D300Y (GAT→TAT) rfaJUDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base G (37/38);  new base T (14/11);  total (51/49)
Fisher's exact test for biased strand distribution p-value = 6.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-01

TATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATATCT  >  minE/2540307‑2540439
                                                                  |                                                                  
tATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGc                                                                >  1:513026/1‑71 (MQ=255)
tATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGc                                                                >  1:132201/1‑71 (MQ=255)
tATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc                                                                >  1:3648802/1‑71 (MQ=255)
 aTCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc                                                                >  1:748756/1‑70 (MQ=255)
         gTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAat                                                       <  1:2049874/71‑1 (MQ=255)
            aaaTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGaaa                                                            >  1:3282430/1‑63 (MQ=255)
            aaaTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattat                                                    >  1:2337842/1‑71 (MQ=255)
              aTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTg                                                  <  1:548684/71‑1 (MQ=255)
              aTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTg                                                  <  1:236384/71‑1 (MQ=255)
               tACTATAAAATAGCTTTAGAAAATTCCCCATGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTg                                                  >  1:258155/1‑70 (MQ=255)
                   ataAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAAtt                                              >  1:190570/1‑70 (MQ=255)
                    taAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTa                                            <  1:2875278/71‑1 (MQ=255)
                    taAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAAttt                                             >  1:1649727/1‑70 (MQ=255)
                    taAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAAttt                                             >  1:204592/1‑70 (MQ=255)
                    taAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAAttt                                             >  1:1089631/1‑70 (MQ=255)
                     aaaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTa                                            >  1:2192964/1‑70 (MQ=255)
                     aaaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTa                                            >  1:1894483/1‑70 (MQ=255)
                          aGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaa                                        >  1:1243544/1‑69 (MQ=255)
                           gCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAg                                     <  1:566678/71‑1 (MQ=255)
                           gCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAg                                     <  1:488526/71‑1 (MQ=255)
                           gCTTTAGAAAATTCCCCCTGGAAAGATGAATCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAg                                     <  1:2447957/71‑1 (MQ=255)
                             tttAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTg                                                  <  1:3518207/56‑1 (MQ=255)
                               tAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGata                                  >  1:3399451/1‑70 (MQ=255)
                               tAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGata                                  <  1:2294622/70‑1 (MQ=255)
                                aGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       <  1:839580/48‑1 (MQ=255)
                                aGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       <  1:3284/48‑1 (MQ=255)
                                aGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       <  1:1492269/48‑1 (MQ=255)
                                aGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       <  1:2786465/48‑1 (MQ=255)
                                 gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCaa                                                        >  1:1679441/1‑46 (MQ=255)
                                 gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                <  1:3479621/70‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc                                                          <  1:3785279/43‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc                                                          <  1:3355752/43‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc                                                          <  1:1299234/43‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc                                                          <  1:1458166/43‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc                                                          <  1:803407/43‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc                                                          <  1:1311409/43‑1 (MQ=255)
                                    aaTTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTa                                            <  1:1820997/55‑1 (MQ=255)
                                    aaTTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAg                                     <  1:867508/62‑1 (MQ=255)
                                    aaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACa                            <  1:3314442/71‑1 (MQ=255)
                                     aTTCCCCCTGGATAGATGACTCTCCACGAGATGCGAAATCAat                                                       >  1:2326702/1‑43 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       >  1:3565020/1‑43 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       >  1:2931303/1‑43 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       >  1:3008180/1‑43 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       >  1:3389701/1‑43 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       >  1:524124/1‑43 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       >  1:1458802/1‑43 (MQ=255)
                                      ttCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATc                          <  1:3428122/71‑1 (MQ=255)
                                      ttCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATc                          <  1:652252/71‑1 (MQ=255)
                                       tCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCt                         >  1:3458611/1‑71 (MQ=255)
                                            cTGGAAAGATGACTCTCCACGAGATGCGAAATCAatt                                                      <  1:3215782/37‑1 (MQ=255)
                                            cTGGAAAGATGACTCTCCACGAGATGCGAAATCAatt                                                      <  1:1500955/37‑1 (MQ=255)
                                            cTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                       <  1:1953263/36‑1 (MQ=255)
                                               gAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTg                  >  1:3539554/1‑70 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaaaa                                      >  1:3797228/1‑50 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     <  1:3403608/67‑1 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc                 <  1:3989410/71‑1 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc                 <  1:3896009/71‑1 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc                 <  1:563749/71‑1 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc                 <  1:2158205/71‑1 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc                 <  1:3405384/71‑1 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc                 <  1:833412/71‑1 (MQ=255)
                                                  aGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCaa               >  1:2485461/1‑70 (MQ=255)
                                                   gATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGa                                    <  1:3446582/48‑1 (MQ=255)
                                                   gATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAca             >  1:3919394/1‑71 (MQ=255)
                                                    aTGACTTTCCACGAGATGCGAAATCAATTATTGaa                                                >  1:3560927/1‑35 (MQ=255)
                                                    aTGACTCTCCACGAGATGCGAAATCAATTATTGaa                                                >  1:4046759/1‑35 (MQ=255)
                                                    aTGACTCTCCACGAGATGCGAAATCAATTATTGaa                                                >  1:934406/1‑35 (MQ=255)
                                                    aTGACTCTCCACGAGATGCGAAATCAATTATTGaa                                                >  1:343720/1‑35 (MQ=255)
                                                    aTGACTCTCCACGAGATGCGAAATCAATTATTGaa                                                >  1:2488755/1‑35 (MQ=255)
                                                    aTGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAca             <  1:1552045/70‑1 (MQ=255)
                                                     tGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGata                                  >  1:1963676/1‑48 (MQ=255)
                                                      gACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatca          >  1:1693763/1‑71 (MQ=255)
                                                      gACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatca          >  1:1553380/1‑71 (MQ=255)
                                                      gACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatca          >  1:33733/1‑71 (MQ=255)
                                                       aCTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatcat         <  1:1156930/71‑1 (MQ=255)
                                                       aCTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatcat         <  1:3233143/71‑1 (MQ=255)
                                                       aCTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatcat         >  1:3835892/1‑71 (MQ=255)
                                                       aCTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatcat         <  1:3067511/71‑1 (MQ=255)
                                                       aCTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatcat         <  1:2751716/71‑1 (MQ=255)
                                                        ctctCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACCTCTTTTACTGCAAcatcat         >  1:440509/1‑70 (MQ=255)
                                                        ctctCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCAtt        <  1:1034828/71‑1 (MQ=255)
                                                        ctctCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCAtt        <  1:650159/71‑1 (MQ=255)
                                                        ctctCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     <  1:1702050/58‑1 (MQ=255)
                                                        ctctCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCAtt        <  1:238846/71‑1 (MQ=255)
                                                          ctcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                       <  1:1731326/54‑1 (MQ=255)
                                                          ctcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                       <  1:287151/54‑1 (MQ=255)
                                                          ctcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                       <  1:3703164/54‑1 (MQ=255)
                                                           tcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtata     >  1:3311433/1‑71 (MQ=255)
                                                           tcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtata     >  1:1772857/1‑71 (MQ=255)
                                                           tcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATta       >  1:3522050/1‑69 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCt                         >  1:2454918/1‑51 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     >  1:556020/1‑55 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     >  1:2446643/1‑55 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     >  1:114762/1‑55 (MQ=255)
                                                            ccACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtata     >  1:4016145/1‑70 (MQ=255)
                                                            ccACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     >  1:1280897/1‑54 (MQ=255)
                                                            ccACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     >  1:929393/1‑54 (MQ=255)
                                                            ccACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                     >  1:2948846/1‑54 (MQ=255)
                                                             cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAtc   >  1:251374/1‑71 (MQ=255)
                                                              aCGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAtct  <  1:3377991/71‑1 (MQ=255)
                                                                  |                                                                  
TATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATATCT  >  minE/2540307‑2540439

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