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
A3 F2 I1 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA Exported 214,925 A→C 70.0% D12A (GAT→GCT)  dnaQ → DNA polymerase III epsilon subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported214,9250AC70.0% 506.5 / 180.1 276D12A (GAT→GCT) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (57/26);  new base C (92/101);  total (149/127)
Fisher's exact test for biased strand distribution p-value = 1.54e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 281 total aligned reads displayed.

AACTGTAAAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCC  >  Exported/214855‑214995
                                                                      |                                                                      
  cTGTAAAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCACGATa                                                                      >  1:1232111/1‑71 (MQ=255)
      aaaaCGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATAcc                                                                    >  1:1461393/1‑69 (MQ=255)
           ctcAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAacca                                                             >  1:73701/3‑71 (MQ=255)
            tcAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                               <  1:397196/67‑1 (MQ=255)
              aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                          >  1:2895135/1‑71 (MQ=255)
                  cTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGaaa                                                                >  1:347227/1‑61 (MQ=255)
                     aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                   >  1:1626572/1‑71 (MQ=255)
                     aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGaa                                                   >  1:2754008/1‑71 (MQ=255)
                     aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGaa                                                   >  1:4197595/1‑71 (MQ=255)
                      cATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                  <  1:1058026/71‑1 (MQ=255)
                      cATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                  <  1:4207633/71‑1 (MQ=255)
                        tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                         <  1:1453806/62‑1 (MQ=255)
                        tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                <  1:2223219/71‑1 (MQ=255)
                        tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                <  1:1976825/71‑1 (MQ=255)
                        tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                <  1:2533216/71‑1 (MQ=255)
                        tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                <  1:1703539/71‑1 (MQ=255)
                        tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAAc                                                  >  1:769434/1‑69 (MQ=255)
                         aaaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                  >  1:5297072/1‑68 (MQ=255)
                          aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGa                                                                        >  1:1316181/1‑45 (MQ=255)
                          aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                  >  1:1597719/1‑67 (MQ=255)
                          aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                  >  1:1760738/1‑67 (MQ=255)
                           aTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGa                                              >  1:4025945/1‑70 (MQ=255)
                              aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                           <  1:1046752/70‑1 (MQ=255)
                               ccGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGt                                         <  1:1802871/71‑1 (MQ=255)
                                cGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTg                                        >  1:1339242/1‑71 (MQ=255)
                                   tATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                      >  1:2773586/1‑70 (MQ=255)
                                    aTGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                    >  1:4932414/1‑71 (MQ=255)
                                    aTGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAaccac                                                            >  1:2148896/1‑47 (MQ=255)
                                    aTGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGATCCAGATTGGTGCGCa                                    >  1:66557/1‑71 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                               <  1:5265950/59‑1 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                               <  1:4833459/59‑1 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                               <  1:3081269/59‑1 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                            <  1:4381817/62‑1 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                            <  1:3829310/62‑1 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                            <  1:3712435/62‑1 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                   <  1:968480/71‑1 (MQ=255)
                                     tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                   <  1:2704918/71‑1 (MQ=255)
                                      gAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                                      <  1:3902611/67‑1 (MQ=255)
                                       aGCACTGCAATTACACGCCAGATCGTTCTCGCTAcc                                                                    >  1:4275133/1‑36 (MQ=255)
                                       aGCACTGCAATTACACGCCAGATCGTTCTCGCTAcc                                                                    >  1:5577126/1‑36 (MQ=255)
                                       aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                 >  1:892572/1‑71 (MQ=255)
                                       aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                 >  1:5433870/1‑71 (MQ=255)
                                        gCACTGCATTTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTa                                 <  1:5624041/70‑1 (MQ=255)
                                        gCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                             <  1:2290870/58‑1 (MQ=255)
                                         cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                               <  1:5182075/71‑1 (MQ=255)
                                         cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                               <  1:3179595/71‑1 (MQ=255)
                                             gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                           >  1:573601/1‑71 (MQ=255)
                                             gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                           >  1:3641491/1‑71 (MQ=255)
                                             gCAATTACACGCCAGATCGTTCTCGATACCGAAaccac                                                            >  1:5359034/1‑38 (MQ=255)
                                             gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTAt                                                      >  1:2186730/1‑44 (MQ=255)
                                              cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                          >  1:5254657/1‑71 (MQ=255)
                                              cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGAACTATGAAGGc                          >  1:3488354/1‑71 (MQ=255)
                                                aTTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                  <  1:2448811/45‑1 (MQ=38)
                                                aTTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                <  1:1849165/63‑1 (MQ=255)
                                                 ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                               <  1:3349360/63‑1 (MQ=255)
                                                 ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                               <  1:4703090/63‑1 (MQ=255)
                                                 ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                               <  1:5153662/63‑1 (MQ=255)
                                                 ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGa                              <  1:3465458/64‑1 (MQ=255)
                                                 ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                       <  1:2071072/71‑1 (MQ=255)
                                                 ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                       <  1:4363118/71‑1 (MQ=255)
                                                  tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                       >  1:2005258/1‑70 (MQ=255)
                                                   acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaaac                                                 >  1:5050722/1‑41 (MQ=37)
                                                   acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                              >  1:812832/1‑46 (MQ=39)
                                                   acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                    >  1:789121/1‑56 (MQ=255)
                                                   acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                             >  1:2206126/1‑63 (MQ=255)
                                                   acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAg                            >  1:4802311/1‑64 (MQ=255)
                                                   acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                       >  1:2396785/1‑69 (MQ=255)
                                                   acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                       >  1:2610468/1‑69 (MQ=255)
                                                   acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                             >  1:2675376/1‑63 (MQ=255)
                                                   acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                             >  1:1494087/1‑63 (MQ=255)
                                                   acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                       >  1:3046517/1‑69 (MQ=255)
                                                     acGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                <  1:343710/58‑1 (MQ=255)
                                                      cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                  <  1:1379114/71‑1 (MQ=255)
                                                         cAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt               <  1:1033091/71‑1 (MQ=255)
                                                          aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                <  1:113424/53‑1 (MQ=255)
                                                          aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                <  1:1102196/53‑1 (MQ=255)
                                                          aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt              <  1:5519357/71‑1 (MQ=255)
                                                           gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt              >  1:484422/1‑70 (MQ=255)
                                                           gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt              >  1:3549883/1‑70 (MQ=255)
                                                            aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                             <  1:4140759/38‑1 (MQ=37)
                                                            aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                <  1:3879901/67‑1 (MQ=255)
                                                             tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGa                              >  1:2313913/1‑52 (MQ=255)
                                                             tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt              >  1:1532179/1‑68 (MQ=255)
                                                             tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga            <  1:2831137/70‑1 (MQ=255)
                                                              cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                             >  1:588952/1‑52 (MQ=255)
                                                                ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt        <  1:4871080/71‑1 (MQ=255)
                                                                  ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                             >  1:4309449/1‑48 (MQ=39)
                                                                  ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg      >  1:3154679/1‑71 (MQ=255)
                                                                  ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg      >  1:1580644/1‑71 (MQ=255)
                                                                   tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                          <  1:4500976/50‑1 (MQ=255)
                                                                   tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                          <  1:3022627/50‑1 (MQ=255)
                                                                   tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                        <  1:4913546/52‑1 (MQ=255)
                                                                   tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                        <  1:1227792/52‑1 (MQ=255)
                                                                   tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGt     >  1:4107906/1‑71 (MQ=255)
                                                                   tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGt     >  1:4234086/1‑71 (MQ=255)
                                                                   tcGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                                      >  1:4647211/1‑38 (MQ=255)
                                                                   tcGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                                      >  1:3580809/1‑38 (MQ=255)
                                                                   tcGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                                      >  1:210453/1‑38 (MQ=255)
                                                                     gATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGc   >  1:3003124/1‑71 (MQ=255)
                                                                      aTACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGt     >  1:476154/1‑68 (MQ=255)
                                                                      |                                                                      
AACTGTAAAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCC  >  Exported/214855‑214995

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