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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,540,373 G→T 35.8% 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
*minE2,540,3730GT35.8% 208.4 / 92.5 117D300Y (GAT→TAT) rfaJUDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base G (42/33);  new base T (19/23);  total (61/56)
Fisher's exact test for biased strand distribution p-value = 3.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

Only 100 of 124 total aligned reads displayed.

TATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATATCTCA  >  minE/2540307‑2540441
                                                                  |                                                                    
 aTCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc                                                                  <  1:1061897/70‑1 (MQ=255)
 aTCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc                                                                  <  1:975268/70‑1 (MQ=255)
 aTCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc                                                                  <  1:2485749/70‑1 (MQ=255)
 aTCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc                                                                  <  1:1132704/70‑1 (MQ=255)
        ggTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCa                                                           >  1:3241231/1‑70 (MQ=255)
        ggTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCaa                                                          >  1:3182360/1‑71 (MQ=255)
        ggTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCaa                                                          >  1:645963/1‑71 (MQ=255)
           aaaaTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                         <  1:3580103/69‑1 (MQ=255)
            aaaTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattat                                                      >  1:1401491/1‑71 (MQ=255)
            aaaTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattat                                                      >  1:2549313/1‑71 (MQ=255)
            aaaTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattat                                                      >  1:1685663/1‑71 (MQ=255)
             aaTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAat                                                         <  1:1073703/67‑1 (MQ=255)
              aTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAattatt                                                     >  1:738845/1‑70 (MQ=255)
               tACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAatta                                                       >  1:4251448/1‑67 (MQ=255)
               tACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAatta                                                       >  1:2756002/1‑67 (MQ=255)
                    taAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTa                                              <  1:3297665/71‑1 (MQ=255)
                     aaaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTa                                              >  1:1649901/1‑70 (MQ=255)
                     aaaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAAtt                                                >  1:3577000/1‑68 (MQ=255)
                      aaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGaaa                                                              >  1:3781814/1‑53 (MQ=255)
                      aaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGaaa                                                              >  1:1752946/1‑53 (MQ=255)
                      aaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaa                                             >  1:813879/1‑70 (MQ=255)
                              ttAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGat                                     >  1:625771/1‑70 (MQ=255)
                               tAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGata                                    >  1:2309475/1‑70 (MQ=255)
                               tAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGata                                    >  1:2463454/1‑70 (MQ=255)
                               tAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGat                                     <  1:820550/69‑1 (MQ=255)
                               tAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGat                                     <  1:2340814/69‑1 (MQ=255)
                                 gAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:2146550/70‑1 (MQ=255)
                                 gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:1706807/70‑1 (MQ=255)
                                 gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:3550939/70‑1 (MQ=255)
                                 gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:1358000/70‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:3329387/69‑1 (MQ=255)
                                  aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattatt                                                     <  1:2537927/50‑1 (MQ=255)
                                    aaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc                                                            >  1:965326/1‑41 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAat                                                         <  1:347072/43‑1 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAat                                                         <  1:2139713/43‑1 (MQ=255)
                                     aTTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACa                              <  1:801769/70‑1 (MQ=255)
                                         ccccTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                         <  1:3435241/71‑1 (MQ=255)
                                         ccccTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                         <  1:3033007/71‑1 (MQ=255)
                                         ccccTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtt                          <  1:339549/70‑1 (MQ=255)
                                          cccTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:500109/61‑1 (MQ=255)
                                          cccTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:685999/61‑1 (MQ=255)
                                           ccTGGAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                       <  1:1486940/71‑1 (MQ=255)
                                            cTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                         >  1:3217869/1‑36 (MQ=255)
                                            cTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                         >  1:2642505/1‑36 (MQ=255)
                                            cTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                         >  1:1767116/1‑36 (MQ=255)
                                            cTGGAAAGATGACTCTCCACGAGATGCGAAATCAat                                                         >  1:2023358/1‑36 (MQ=255)
                                             tGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt                        <  1:1912009/68‑1 (MQ=255)
                                             tGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt                        <  1:548321/68‑1 (MQ=255)
                                             tGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGt                     >  1:2862189/1‑71 (MQ=255)
                                              ggAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTaaaa                                           <  1:876441/48‑1 (MQ=255)
                                              ggAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTaaaa                                           <  1:1062933/48‑1 (MQ=255)
                                              ggAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:1888071/57‑1 (MQ=255)
                                              ggAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:2174621/57‑1 (MQ=255)
                                              ggAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:4215231/57‑1 (MQ=255)
                                              ggAAAGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:2268311/57‑1 (MQ=255)
                                              ggAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTg                    >  1:721953/1‑71 (MQ=255)
                                              ggAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTg                    >  1:2254235/1‑71 (MQ=255)
                                              ggAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTg                    >  1:4186541/1‑71 (MQ=255)
                                               gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaaa                                         >  1:3691340/1‑49 (MQ=255)
                                               gAAAGATGACTCT‑CACGAGATGCGAAATCAATTATTGAATTTaaaaaaa                                        >  1:143867/1‑49 (MQ=255)
                                                aaaGATGACTCTCCACGATATGCGAAATCAATTATTGAATTTaaaaaa                                         >  1:1785319/1‑48 (MQ=255)
                                                   gATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAca               <  1:2453596/71‑1 (MQ=255)
                                                   gATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAca               <  1:3836300/71‑1 (MQ=255)
                                                     tGACTCTCCAAGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                       <  1:3027533/61‑1 (MQ=255)
                                                       aCTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatcat           <  1:3521369/71‑1 (MQ=255)
                                                        ctctCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCAtt          <  1:1163727/71‑1 (MQ=255)
                                                         tctcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt                        <  1:3297451/56‑1 (MQ=255)
                                                         tctcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt                        <  1:2970091/56‑1 (MQ=255)
                                                         tctcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt                        <  1:4135015/56‑1 (MQ=255)
                                                         tctcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt                        <  1:1806282/56‑1 (MQ=255)
                                                         tctcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa                       >  1:4001206/1‑57 (MQ=255)
                                                          ctcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:3715725/45‑1 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGatat                                   <  1:1593438/43‑1 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGatat                                   <  1:113311/43‑1 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACAt                             <  1:2892802/49‑1 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACAt                             <  1:2202580/49‑1 (MQ=255)
                                                           tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGt                     >  1:3066720/1‑57 (MQ=255)
                                                            ccACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaaa                                >  1:559494/1‑45 (MQ=255)
                                                            ccACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaaa                                >  1:3917439/1‑45 (MQ=255)
                                                             cACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatc             >  1:398950/1‑63 (MQ=255)
                                                             cACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAcatc             >  1:1147504/1‑63 (MQ=255)
                                                             cACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAc                >  1:2729721/1‑60 (MQ=255)
                                                             cACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAAc                >  1:1508148/1‑60 (MQ=255)
                                                             cACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAtc     >  1:1070217/1‑71 (MQ=255)
                                                             cACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAtc     >  1:2519501/1‑71 (MQ=255)
                                                             cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaa                                 >  1:3447830/1‑43 (MQ=255)
                                                             cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaa                                 >  1:2656842/1‑43 (MQ=255)
                                                             cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtt                          >  1:1560470/1‑50 (MQ=255)
                                                             cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtat        <  1:479006/68‑1 (MQ=255)
                                                             cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtat        <  1:4041291/68‑1 (MQ=255)
                                                               cGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAtct    >  1:1898831/1‑70 (MQ=255)
                                                               cGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAtct    >  1:1833663/1‑70 (MQ=255)
                                                               cGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAtct    >  1:1016761/1‑70 (MQ=255)
                                                                gagaTGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATATCTCa  <  1:3808719/71‑1 (MQ=255)
                                                                gagaTGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATATCTCa  <  1:1391220/71‑1 (MQ=255)
                                                                 agaTGCGAAATCTATTATTGTATTTAAAAAAAGATATAAACATCttt                         <  1:958054/47‑1 (MQ=255)
                                                                 agaTGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                         <  1:423686/47‑1 (MQ=255)
                                                                 agaTGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                         <  1:3162240/47‑1 (MQ=255)
                                                                 agaTGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt                         <  1:2683444/47‑1 (MQ=255)
                                                                  gaTGCGAAATCAATTATTGAATTTAAAAAAAGAtata                                  <  1:1685755/37‑1 (MQ=255)
                                                                  |                                                                    
TATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATATCTCA  >  minE/2540307‑2540441

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