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
A18 F999 I0 R1 72 114.7 9135302 95.6% 8733348 49.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,801,078 (T)7→6 coding (922/1017 nt) waaJ ← UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,801,0720T.96.7% 786.2 / 24.7 179coding (928/1017 nt)waaJUDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (2/4);  new base . (95/78);  total (97/82)
Fisher's exact test for biased strand distribution p-value = 4.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.90e-01

Only 100 of 218 total aligned reads displayed.

GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117
                                                 |                                             
 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:1527180/1‑50 (MQ=255)
 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              <  1:1969886/50‑1 (MQ=255)
 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  2:2505472/49‑1 (MQ=255)
 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  1:4398554/49‑1 (MQ=255)
 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  1:277949/49‑1 (MQ=255)
 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               <  1:3726705/49‑1 (MQ=255)
  tataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             >  2:188321/1‑50 (MQ=255)
  tataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             >  2:486375/1‑50 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           <  2:3715766/50‑1 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           <  2:1049585/50‑1 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             <  2:1298024/48‑1 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt                                             <  1:4122464/48‑1 (MQ=255)
       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:3996994/50‑3 (MQ=255)
         ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                                      >  1:3878477/1‑49 (MQ=255)
         ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa                                       <  1:1013202/49‑1 (MQ=255)
         ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa                                       <  2:3153927/49‑1 (MQ=255)
          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                                      <  1:3564250/49‑2 (MQ=255)
          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  2:4444587/1‑50 (MQ=255)
          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    <  2:3522574/50‑1 (MQ=255)
          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:2395419/1‑50 (MQ=255)
           tGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    >  1:3582864/1‑49 (MQ=39)
            gagaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                   >  1:1116982/1‑49 (MQ=39)
             agaTATAATGATGTTGCGCTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:1263672/49‑1 (MQ=38)
             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                   <  1:1308106/48‑1 (MQ=39)
             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa                                 >  2:1214986/1‑50 (MQ=255)
             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:434230/49‑1 (MQ=39)
             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:3134695/49‑1 (MQ=39)
              gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                <  1:2076197/50‑1 (MQ=255)
               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata                               <  1:269093/50‑1 (MQ=255)
               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata                               <  2:2712473/50‑1 (MQ=255)
               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                >  1:286330/1‑49 (MQ=39)
               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                >  1:1776608/1‑49 (MQ=39)
                tataATGATGTTGCACTAACAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  2:891024/1‑50 (MQ=255)
                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  2:2762764/1‑50 (MQ=255)
                 ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             >  2:1928896/1‑50 (MQ=255)
                 ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             >  2:3006511/1‑50 (MQ=255)
                  taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             <  1:3611144/49‑1 (MQ=39)
                   aaTGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                            >  2:4073212/1‑49 (MQ=39)
                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  2:3113489/49‑1 (MQ=39)
                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGa                          <  1:1891246/50‑1 (MQ=255)
                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGa                          <  2:1145351/50‑1 (MQ=255)
                    atgatgGTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  2:2808421/49‑1 (MQ=38)
                     tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt                         <  1:2178699/50‑1 (MQ=255)
                      gatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        >  2:4114692/1‑50 (MQ=255)
                      gatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        >  1:3910374/1‑50 (MQ=255)
                      gatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        >  1:2675778/1‑50 (MQ=255)
                      gatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        >  2:762513/1‑50 (MQ=255)
                       atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt                       <  2:4386332/50‑1 (MQ=255)
                       atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt                       <  1:4128242/50‑1 (MQ=255)
                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      >  1:735441/1‑50 (MQ=255)
                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      <  1:1041535/50‑1 (MQ=255)
                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      <  1:4551425/50‑1 (MQ=255)
                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      <  1:3285969/50‑1 (MQ=255)
                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      >  1:3511205/1‑50 (MQ=255)
                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg                     <  2:845179/49‑1 (MQ=39)
                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGc                    <  1:3398190/50‑1 (MQ=255)
                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGc                    <  1:99180/50‑1 (MQ=255)
                           tGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa                   >  2:4527046/1‑50 (MQ=255)
                           tGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa                   >  2:1409766/1‑50 (MQ=255)
                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa                   <  2:3307928/49‑1 (MQ=39)
                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa                   <  2:443701/49‑1 (MQ=39)
                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa                   <  1:3821221/49‑1 (MQ=39)
                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa                   <  1:4322677/49‑1 (MQ=39)
                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  1:1467022/1‑50 (MQ=255)
                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  2:2312650/1‑50 (MQ=255)
                             cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc                 <  1:2552865/50‑1 (MQ=255)
                             cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc                 >  2:2056615/1‑50 (MQ=255)
                             cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  <  1:1367228/49‑1 (MQ=39)
                              aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                <  1:2346901/50‑1 (MQ=255)
                              aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                >  2:3433039/1‑50 (MQ=255)
                              aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                <  1:2025738/50‑1 (MQ=255)
                              aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct                >  1:561622/1‑50 (MQ=255)
                               cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc               <  2:2990377/50‑1 (MQ=255)
                               cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc               <  1:3340126/50‑1 (MQ=255)
                               cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc               <  1:171371/50‑1 (MQ=255)
                                gaaaaGATGTTTATATC‑TTTGTTAAATGCAAGAAGTGATTACGCAtct                <  2:2924424/47‑1 (MQ=255)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              <  1:3043842/48‑1 (MQ=39)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              <  2:813524/48‑1 (MQ=39)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg              <  1:3666432/48‑1 (MQ=39)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             <  2:2156897/49‑1 (MQ=39)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  2:2974786/1‑50 (MQ=255)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  2:915101/1‑50 (MQ=255)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  2:1807883/1‑50 (MQ=255)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:3256996/1‑50 (MQ=255)
                                   aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  2:1507857/1‑49 (MQ=39)
                                    aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:4483466/1‑48 (MQ=39)
                                    aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:119815/1‑48 (MQ=39)
                                     gATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            >  1:3002590/1‑47 (MQ=39)
                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgaga        <  1:2019817/50‑1 (MQ=255)
                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgaga        <  2:2565673/50‑1 (MQ=255)
                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga          >  2:4332219/1‑48 (MQ=39)
                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga          >  2:2138737/1‑48 (MQ=39)
                                        gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  2:1593275/1‑50 (MQ=255)
                                        gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:3385074/1‑50 (MQ=255)
                                        gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      >  1:2250866/1‑50 (MQ=255)
                                         tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt      <  1:1982379/49‑1 (MQ=39)
                                         tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTc     <  1:1600570/50‑1 (MQ=255)
                                         tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTc     <  2:3887133/50‑1 (MQ=255)
                                          ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    >  1:3422767/1‑50 (MQ=255)
                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:57768/1‑50 (MQ=255)
                                                 |                                             
GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A