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 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 236,107 A→C 54.1% 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.gb236,1070AC54.1% 145.6 / 145.4 137E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (44/19);  new base C (40/34);  total (84/53)
Fisher's exact test for biased strand distribution p-value = 7.83e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

Only 100 of 142 total aligned reads displayed.

ACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTG  >  W3110S.gb/236040‑236175
                                                                   |                                                                    
aCGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGaa                                                                     >  1:1413561/1‑69 (MQ=255)
    cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAacca                                                                 >  1:1981684/1‑69 (MQ=255)
    cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAacca                                                                 >  1:3695156/1‑69 (MQ=255)
     aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAaccac                                                                >  1:2380919/1‑69 (MQ=255)
          tGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGt                                                            >  1:2355879/1‑68 (MQ=255)
          tGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGt                                                            >  1:2774683/1‑68 (MQ=255)
                 aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGa                                                        >  1:144536/1‑65 (MQ=255)
                 aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                    <  1:1747720/69‑1 (MQ=255)
                 aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                    <  1:2467139/69‑1 (MQ=255)
                 aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                    <  1:3300812/69‑1 (MQ=255)
                 aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                    <  1:700330/69‑1 (MQ=255)
                 aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGa                                                        >  1:1111395/1‑65 (MQ=255)
                 aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCa                                                    <  1:3344565/69‑1 (MQ=255)
                    gACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGAt                                                 <  1:3696203/69‑1 (MQ=255)
                      ccGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTg                                               >  1:2962867/1‑69 (MQ=255)
                         cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTg                                            <  1:1051605/69‑1 (MQ=255)
                          tATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTg                                            >  1:1122370/1‑68 (MQ=255)
                              aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                             <  1:2302443/47‑1 (MQ=255)
                              aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                             <  1:2154716/47‑1 (MQ=255)
                              aGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCAc                                       >  1:3067210/1‑69 (MQ=255)
                              aGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCAc                                       >  1:2110450/1‑69 (MQ=255)
                               gCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACt                                      >  1:3498605/1‑69 (MQ=255)
                                  cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:3274242/69‑1 (MQ=255)
                                  cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:864783/69‑1 (MQ=255)
                                  cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:87742/69‑1 (MQ=255)
                                  cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:2160331/69‑1 (MQ=255)
                                  cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:3000520/69‑1 (MQ=255)
                                   tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:1798760/68‑1 (MQ=255)
                                   tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:1596566/68‑1 (MQ=255)
                                   tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGa                                  <  1:591966/69‑1 (MQ=255)
                                    gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                         >  1:3085739/1‑45 (MQ=38)
                                    gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGa                                                        >  1:359687/1‑46 (MQ=39)
                                    gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGa                                                        >  1:1614984/1‑46 (MQ=39)
                                    gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                 <  1:3078235/69‑1 (MQ=255)
                                     cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTgc                                           >  1:1958405/1‑58 (MQ=255)
                                     cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAg                                >  1:2013725/1‑69 (MQ=255)
                                     cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAg                                >  1:3090507/1‑69 (MQ=255)
                                      aaTTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATg                                                         <  1:2527769/43‑1 (MQ=255)
                                         tACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGAtt                                                >  1:2889193/1‑49 (MQ=255)
                                         tACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGAt                                                 >  1:2365547/1‑48 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAcc                                                     >  1:1833942/1‑43 (MQ=38)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAcc                                                     >  1:2745267/1‑43 (MQ=38)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:3153695/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:1521795/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:1349508/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:2973820/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:2391838/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:3021937/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:2387550/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:2491961/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:904167/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:2773201/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:3526036/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:1852498/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:1933431/1‑61 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:2531525/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:1059968/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:2169406/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                             >  1:601957/1‑67 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:3455320/69‑1 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:3161961/69‑1 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:1911443/69‑1 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:2013471/69‑1 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:529995/69‑1 (MQ=255)
                                          acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:2941121/69‑1 (MQ=255)
                                          acacGCAAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:2086726/1‑61 (MQ=255)
                                               ccAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                      <  1:1274518/69‑1 (MQ=255)
                                                   aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:192242/1‑67 (MQ=255)
                                                   aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:688755/1‑67 (MQ=255)
                                                    tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:3108386/51‑1 (MQ=255)
                                                    tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:435282/1‑66 (MQ=255)
                                                    tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:1413121/1‑66 (MQ=255)
                                                    tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:3294571/1‑66 (MQ=255)
                                                    tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:1441975/1‑66 (MQ=255)
                                                     cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:3432525/50‑1 (MQ=255)
                                                     cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:1240556/50‑1 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACt                                      >  1:1821767/1‑47 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACt                                      >  1:3209875/1‑47 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACt                                      >  1:759057/1‑47 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACt                                      >  1:2338043/1‑47 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:829698/50‑1 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:1147291/50‑1 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:67611/50‑1 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:760367/58‑1 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:2117898/58‑1 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:95241/1‑65 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    >  1:3076890/1‑65 (MQ=255)
                                                     cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                <  1:78533/69‑1 (MQ=255)
                                                      gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag               >  1:926675/1‑69 (MQ=255)
                                                      gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag               >  1:3515202/1‑69 (MQ=255)
                                                        tctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt             >  1:105902/1‑69 (MQ=255)
                                                        tctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt             <  1:2167592/69‑1 (MQ=255)
                                                         ctcGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                      <  1:925680/59‑1 (MQ=255)
                                                         ctcGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt            >  1:1108024/1‑69 (MQ=255)
                                                            gATACCGAAACCACCGGTATGAACCAGATTGGTGCGCTCTATGAAgg                               >  1:2057118/1‑47 (MQ=255)
                                                            gATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   >  1:2192536/1‑43 (MQ=255)
                                                            gATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGt         >  1:3600526/1‑69 (MQ=255)
                                                              tACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg          <  1:2148515/66‑1 (MQ=255)
                                                                   aaaCCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTg  <  1:469666/69‑1 (MQ=255)
                                                                   aaaCCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTg  <  1:9734/69‑1 (MQ=255)
                                                                   |                                                                    
ACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTG  >  W3110S.gb/236040‑236175

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