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
A1 F1 I0 R1 92 46.1 3712835 96.9% 3597737 60.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 236,107 A→C 92.0% E14A (GAA→GCA)  dnaQ → DNA polymerase III epsilon subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb236,1070AC92.0% 3559.0 / 127.2 1106E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (43/47);  new base C (540/475);  total (584/522)
Fisher's exact test for biased strand distribution p-value = 3.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 1139 total aligned reads displayed.

AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTGAA  >  W3110S.gb/236038‑236177
                                                                     |                                                                      
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                      >  1:5949‑M2/6‑71 (MQ=255)
      cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAaccacc                                                                 >  1:869411/1‑71 (MQ=255)
      cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAaccacc                                                                 >  1:1829132/1‑71 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                                >  1:3617369/1‑71 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACAGCAaccac                                                                  <  1:733940/69‑1 (MQ=255)
           cTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                      >  1:320071/1‑61 (MQ=255)
            tGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTa                                                             >  1:1109523/1‑69 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATTAACCa                                                      <  1:2599302/71‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                      <  1:1528216/71‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                      <  1:493409/71‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAAc                                                        >  1:2345657/1‑69 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAcc                                                       >  1:1775808/1‑68 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                        >  1:666170/1‑67 (MQ=255)
                    aTGCCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                   >  1:168447/1‑71 (MQ=255)
                     tGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                                  >  1:1385970/1‑71 (MQ=255)
                     tGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                                  <  1:3654205/71‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                                 <  1:2783997/70‑1 (MQ=255)
                        ccGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGTACCAGATTGGt                                               <  1:2721946/71‑1 (MQ=255)
                          gCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgc                                             <  1:3506040/71‑1 (MQ=255)
                           cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                            >  1:2856678/1‑71 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                         <  1:201281/71‑1 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                      >  1:2748287/1‑40 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                         >  1:1973063/1‑53 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                                     >  1:2666536/1‑57 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                       >  1:1656735/1‑71 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                       >  1:3481847/1‑71 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                           >  1:1230945/1‑49 (MQ=39)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                      <  1:3695983/54‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                     <  1:3180839/71‑1 (MQ=255)
                                   aCTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                     >  1:1154004/1‑70 (MQ=255)
                                    cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                   <  1:2944544/55‑1 (MQ=255)
                                     tGCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                                     <  1:2370636/36‑1 (MQ=38)
                                     tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                    >  1:892384/1‑53 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                                 >  1:1294604/1‑71 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                                 >  1:244314/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                    >  1:1501166/1‑51 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                   >  1:765650/1‑52 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                                >  1:2150270/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                                >  1:1750459/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                                <  1:1586239/71‑1 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                                >  1:2633109/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGa                                                    >  1:2309419/1‑51 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                                     <  1:832674/47‑1 (MQ=39)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                                  <  1:620340/50‑1 (MQ=255)
                                            acagGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                             >  1:2204832/1‑69 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGt                                               >  1:3138057/1‑51 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                             >  1:3302547/1‑69 (MQ=255)
                                            acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                             >  1:953784/1‑69 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAg                          <  1:462835/71‑1 (MQ=255)
                                              acGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATTaa                                   <  1:915004/61‑1 (MQ=255)
                                              acGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGCCCACAAGa                         <  1:2818373/71‑1 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                    >  1:1211358/1‑42 (MQ=38)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                                  <  1:533647/44‑1 (MQ=38)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                        >  1:1706552/1‑70 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                       <  1:1619329/71‑1 (MQ=255)
                                                 ccAGATCGTTCTCGCTACCTCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                      <  1:1056225/71‑1 (MQ=255)
                                                 ccAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                      <  1:1275879/71‑1 (MQ=255)
                                                  cAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt                     >  1:2100556/1‑71 (MQ=255)
                                                  cAGATCGTTCTCGCTACCGCAACCACAGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt                     >  1:3240075/1‑71 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                     <  1:708200/54‑1 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                      >  1:387283/1‑69 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                    <  1:3541113/71‑1 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                    <  1:2414823/71‑1 (MQ=255)
                                                   aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                    <  1:2041977/71‑1 (MQ=255)
                                                    gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                                  <  1:2276341/40‑1 (MQ=38)
                                                    gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                                <  1:1870081/58‑1 (MQ=255)
                                                    gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                             <  1:1001116/61‑1 (MQ=255)
                                                    gATCGTTCTCGATACCGAAACCACCGGTATGAACCAGa                                                    >  1:1185652/1‑38 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTTCGCACTATGAAGGCCACAAGATCATTga                  <  1:2983067/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                   >  1:1472322/1‑54 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                    >  1:805553/1‑69 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                  <  1:194363/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                  <  1:3415955/71‑1 (MQ=255)
                                                      tCGTTCTCGCTAGCGCAACCACCGGTATGAACCAGATTgg                                                >  1:1327086/1‑40 (MQ=37)
                                                      tCGTTCTCGCTACCGCAACCACCGTTATGAACCAGAtt                                                  <  1:2228789/38‑1 (MQ=25)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                   >  1:789545/1‑37 (MQ=37)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                   <  1:2886538/37‑1 (MQ=37)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                      >  1:1354301/1‑50 (MQ=255)
                                                      tCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                     >  1:2481586/1‑51 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                     <  1:2555333/50‑1 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                           >  1:1908976/1‑60 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                        <  1:1081787/63‑1 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                    >  1:41461/1‑67 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                    >  1:3027244/1‑67 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                    >  1:1435969/1‑67 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAta                    >  1:1555487/1‑66 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                                  <  1:2510591/35‑1 (MQ=37)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                      <  1:3267653/63‑1 (MQ=255)
                                                         ttCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt              <  1:1570084/71‑1 (MQ=255)
                                                          tctcGCTACCGCAACCACCGGTATGAACCAGATTGGTTCGCACTATGAAGGCCACAAGATCATTGAGAtt              >  1:2687855/1‑70 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                      >  1:309579/1‑45 (MQ=38)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAg                                  >  1:2902040/1‑49 (MQ=39)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                              >  1:3330497/1‑53 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg            >  1:1804627/1‑71 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                      >  1:3367454/3‑58 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGc         <  1:2184412/69‑1 (MQ=255)
                                                               aTACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTg                   <  1:3447196/60‑1 (MQ=255)
                                                                tACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                           <  1:3591965/51‑1 (MQ=255)
                                                                  ccGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                  <  1:570312/58‑1 (MQ=255)
                                                                  ccGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGtt     >  1:307592/1‑71 (MQ=255)
                                                                     |                                                                      
AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTGAA  >  W3110S.gb/236038‑236177

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