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 R2 532 47.8 3863072 94.9% 3666055 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 94.7% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,809,5810GA94.7% 2596.4 / 88.5 913G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (17/32);  new base A (401/463);  total (418/495)
Fisher's exact test for biased strand distribution p-value = 1.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

Only 100 of 923 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTT  >  W3110S.gb/2809513‑2809648
                                                                    |                                                                   
 cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                  <  1:1816690/71‑1 (MQ=255)
 cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                  <  1:231254/71‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                  <  1:1717666/68‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                 <  1:775133/69‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                               <  1:3728365/71‑1 (MQ=255)
      cTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                               >  1:235014/1‑69 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                               >  1:2545952/1‑68 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                            >  1:3533837/1‑69 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                            <  1:3504159/69‑1 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                             <  1:1857005/68‑1 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                          >  1:880986/1‑71 (MQ=255)
           catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                        <  1:2811704/71‑1 (MQ=255)
           catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                         <  1:2859421/70‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGTGAATTAACGAGACgttgtt                                                    <  1:622119/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                           >  1:3327716/1‑64 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    >  1:2260421/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    >  1:2958963/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    >  1:1631821/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    <  1:2483895/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    <  1:1780918/71‑1 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                  <  1:3602116/71‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                 <  1:578143/71‑1 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                     <  1:1990875/66‑1 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                   <  1:1968040/68‑1 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                <  1:951270/71‑1 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                >  1:1141394/1‑71 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                >  1:1442429/1‑70 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGTGAATTAACGAGACGTTGTTTATgg                                               <  1:1657855/70‑1 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                  >  1:412576/1‑67 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                              >  1:3676094/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                              >  1:3570052/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                              >  1:1469178/1‑71 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                 >  1:2019188/1‑67 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    >  1:2891417/1‑63 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                  >  1:222800/1‑65 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                           >  1:1386279/1‑71 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                        <  1:3240063/71‑1 (MQ=255)
                            agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                        >  1:1758784/1‑70 (MQ=255)
                            agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                        >  1:811422/1‑70 (MQ=255)
                              ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                     <  1:2988494/71‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                    <  1:3203221/69‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                    <  1:854395/69‑1 (MQ=255)
                                  tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                               <  1:2409800/57‑1 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                 >  1:1916140/1‑70 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    >  1:1690244/1‑50 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                     >  1:3277094/1‑49 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                 <  1:1213778/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                 <  1:2060812/69‑1 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                  >  1:251747/1‑50 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                      >  1:2783382/1‑61 (MQ=255)
                                        aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                           <  1:2651772/71‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                           <  1:481165/54‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                               >  1:3136073/1‑66 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    <  1:3450137/44‑1 (MQ=255)
                                           gCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                           >  1:502686/1‑36 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                          <  1:918340/68‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    <  1:2934247/42‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                                        >  1:3421420/1‑38 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     <  1:3077332/71‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    <  1:666010/39‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                          <  1:1004958/49‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                        <  1:3785690/51‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                        <  1:559687/51‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                          <  1:2585835/65‑1 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                   >  1:1504078/1‑71 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                   <  1:716453/38‑1 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                 >  1:3302767/1‑40 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                              >  1:1548056/1‑43 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                   <  1:1080952/70‑1 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                  >  1:3829451/1‑71 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                  >  1:2723369/1‑71 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                             >  1:1602794/1‑43 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc                 <  1:443811/71‑1 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    <  1:3177351/35‑1 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                  >  1:2186701/1‑37 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGTGTCTCAGGAAAACca                <  1:2752683/71‑1 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc                 >  1:2115498/1‑69 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac               <  1:738119/71‑1 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                >  1:117715/1‑70 (MQ=255)
                                                     gCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                         >  1:1406190/1‑44 (MQ=255)
                                                     gCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                >  1:3480277/1‑69 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                >  1:1293111/1‑36 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca              <  1:3109688/70‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac               >  1:214861/1‑69 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGt            >  1:2440545/1‑69 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa           <  1:3630929/70‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa           <  1:3364426/70‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa           <  1:534924/70‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt          >  1:1043619/1‑71 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt          <  1:1102305/71‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt          <  1:3761741/71‑1 (MQ=255)
                                                          aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt         >  1:2384100/1‑71 (MQ=255)
                                                           ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa           >  1:3037681/1‑68 (MQ=255)
                                                           ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt         >  1:2457233/1‑70 (MQ=255)
                                                           ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt         >  1:3152162/1‑70 (MQ=255)
                                                           ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTc        <  1:1880445/71‑1 (MQ=255)
                                                           ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTc        <  1:1341387/71‑1 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa           <  1:2684321/63‑1 (MQ=255)
                                                                 gggaATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     <  1:2569208/52‑1 (MQ=255)
                                                                 gggaATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCtt  <  1:1243952/71‑1 (MQ=255)
                                                                    |                                                                   
ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTT  >  W3110S.gb/2809513‑2809648

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