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 F8 I0 R2 422 46.8 3726540 94.7% 3529033 61.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 236,107 A→C 73.2% 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.gb236,1070AC73.2% 727.2 / 172.0 294E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (47/32);  new base C (134/81);  total (181/113)
Fisher's exact test for biased strand distribution p-value = 6.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.14e-01

Only 100 of 316 total aligned reads displayed.

AACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCG  >  W3110S.gb/236039‑236172
                                                                    |                                                                 
caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                 >  1:941619‑M2/6‑71 (MQ=255)
caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                 >  1:846831‑M2/6‑71 (MQ=255)
caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                 >  1:1807082‑M2/6‑71 (MQ=255)
  actCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                 >  1:764150‑M2/4‑69 (MQ=255)
   ctCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAacca                                                              >  1:2397605‑M2/3‑71 (MQ=255)
   ctCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAacca                                                              >  1:1425245‑M2/3‑71 (MQ=255)
       aGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                          <  1:3288351/71‑1 (MQ=255)
       aGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                          <  1:398345/71‑1 (MQ=255)
         tCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                          <  1:1928921/69‑1 (MQ=255)
           tGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTAt                                                       >  1:2435564/1‑70 (MQ=255)
             aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                      <  1:1163781/69‑1 (MQ=255)
              cATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                   >  1:2163127/1‑71 (MQ=255)
              cATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                   >  1:35316/1‑71 (MQ=255)
                 aaaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                   >  1:1875698/1‑68 (MQ=255)
                  aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAac                                                                >  1:1795326/1‑54 (MQ=255)
                  aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAAc                                                   >  1:2788374/1‑67 (MQ=255)
                   aTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                              <  1:3439263/71‑1 (MQ=255)
                   aTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                              <  1:2937351/71‑1 (MQ=255)
                      aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTgg                                           >  1:264529/1‑71 (MQ=255)
                      aCCGCTATAAGCACTGCAATTTCACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                           <  1:2220966/71‑1 (MQ=255)
                       ccGCTATGAGCACTGCAATTTCACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                           <  1:146195/70‑1 (MQ=255)
                           tATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTa                                                        >  1:1584770/1‑53 (MQ=255)
                           tATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTa                                                        >  1:1599237/1‑53 (MQ=255)
                             taaGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                       <  1:1239401/66‑1 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                          <  1:2893241/47‑1 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:323623/1‑71 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:3506562/1‑71 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:3005977/1‑71 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:1257481/1‑71 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:2104170/1‑71 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:2143100/1‑71 (MQ=255)
                               aGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:1101205/1‑71 (MQ=255)
                                 cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                 >  1:3193096/1‑70 (MQ=255)
                                 cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                 >  1:2913970/1‑70 (MQ=255)
                                    tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                <  1:161834/68‑1 (MQ=255)
                                     gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                            >  1:2970282/1‑71 (MQ=255)
                                     gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                            >  1:3713714/1‑71 (MQ=255)
                                     gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                            >  1:3463021/1‑71 (MQ=255)
                                      cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                              >  1:3392198/1‑68 (MQ=255)
                                      cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                              >  1:837833/1‑68 (MQ=255)
                                      cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                              >  1:1003215/1‑68 (MQ=255)
                                      cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                           >  1:1048058/1‑71 (MQ=255)
                                      cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                           >  1:638408/1‑71 (MQ=255)
                                      cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                           >  1:1670356/1‑71 (MQ=255)
                                         ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                       <  1:1352108/56‑1 (MQ=255)
                                         ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                       <  1:3077868/56‑1 (MQ=255)
                                         ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        <  1:3268994/71‑1 (MQ=255)
                                         ttACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTAtt                                <  1:105857/63‑2 (MQ=255)
                                         ttACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                <  1:8129/63‑1 (MQ=255)
                                         ttACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                <  1:17509/63‑1 (MQ=255)
                                          tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                   >  1:332254/1‑43 (MQ=38)
                                          tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                   >  1:2821616/1‑43 (MQ=38)
                                          tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:2462330/1‑70 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCAGCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:2997038/1‑69 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcgc                                      >  1:3617658/1‑55 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                     >  1:916755/1‑56 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                     >  1:520077/1‑56 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATTAAGGCcac                        >  1:2254663/1‑69 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:450043/1‑69 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:3564461/1‑69 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:1643404/1‑69 (MQ=255)
                                           acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:2832416/1‑69 (MQ=255)
                                           acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:2507514/1‑69 (MQ=255)
                                           acacGCCAGATCGTTCACGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        >  1:1474300/1‑69 (MQ=255)
                                               gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                  <  1:2712066/71‑1 (MQ=255)
                                               gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                  <  1:2181659/71‑1 (MQ=255)
                                               gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                  <  1:3155817/71‑1 (MQ=255)
                                                   gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTg              <  1:592400/71‑1 (MQ=255)
                                                   gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTg              <  1:3493752/71‑1 (MQ=255)
                                                    aTCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                 <  1:2628541/35‑1 (MQ=37)
                                                    aTCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                 <  1:131249/35‑1 (MQ=37)
                                                    aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCTCACTATGAAGGcctc                        <  1:131663/60‑3 (MQ=255)
                                                    aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                        <  1:3547009/60‑1 (MQ=255)
                                                    aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:737657/1‑69 (MQ=255)
                                                    aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:54640/1‑69 (MQ=255)
                                                    aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCAc                                    <  1:1984382/48‑1 (MQ=255)
                                                    aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCAc                                    <  1:1950678/48‑1 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                   >  1:500589/1‑64 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                   >  1:1523183/1‑64 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                   >  1:888270/1‑64 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                   >  1:1185168/1‑64 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:1386091/1‑68 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:3653647/1‑68 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:3369043/1‑68 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag            <  1:231638/71‑1 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag            <  1:2556511/71‑1 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag            <  1:1568609/71‑1 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag            <  1:259411/71‑1 (MQ=255)
                                                     tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag            <  1:1660041/71‑1 (MQ=255)
                                                     tCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag            <  1:1294965/71‑1 (MQ=255)
                                                      cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:710806/1‑67 (MQ=255)
                                                      cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag            <  1:2361939/70‑1 (MQ=255)
                                                      cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:2345376/1‑67 (MQ=255)
                                                      cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt               >  1:2684028/1‑67 (MQ=255)
                                                      cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGAGCACTATGAAGGCCACAAGATCAtt               >  1:686959/1‑67 (MQ=255)
                                                      cGTTCTCGATACCGAAACCAACGGTATGAACCAGATTGGTGCGCa                                     >  1:2812538/1‑45 (MQ=255)
                                                       gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt          <  1:3599296/71‑1 (MQ=255)
                                                        ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                  >  1:2024648/1‑46 (MQ=39)
                                                        ttCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt         <  1:1092266/71‑1 (MQ=255)
                                                          ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg       >  1:3290531/1‑71 (MQ=255)
                                                                    |                                                                 
AACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCG  >  W3110S.gb/236039‑236172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A