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
A5 F8 I0 R2 53 71.6 5374071 98.5% 5293459 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 45.0% 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.gb2,809,5810GA45.0% 51.9 / 176.0 129G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (30/41);  new base A (22/36);  total (52/77)
Fisher's exact test for biased strand distribution p-value = 7.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

Only 100 of 132 total aligned reads displayed.

CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  W3110S.gb/2809514‑2809650
                                                                   |                                                                     
cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                    <  1:1820980/71‑1 (MQ=255)
 tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                    >  1:1088827/1‑70 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                  <  1:5310981/70‑1 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:2735286/71‑1 (MQ=255)
     cTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:2888758/1‑69 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:4897229/1‑68 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                             <  1:1579508/70‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                              <  1:1251047/69‑1 (MQ=255)
            tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                        >  1:4851397/1‑71 (MQ=255)
            tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                        >  1:2822300/1‑71 (MQ=255)
             gtgcatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                          <  1:4181090/65‑1 (MQ=255)
             gtgcatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                          <  1:3986476/65‑1 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                       >  1:3194843/1‑71 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgtt                                                         <  1:3251972/69‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                       <  1:3708117/70‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                       <  1:2272291/70‑1 (MQ=255)
               gcatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                        >  1:1882089/2‑68 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                     <  1:5318669/71‑1 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                     <  1:1104651/71‑1 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    <  1:1499967/71‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                      <  1:3325709/52‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:3996436/1‑61 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                   <  1:3289204/70‑1 (MQ=255)
                   gcaAAGCAATCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                                 >  1:4114780/1‑71 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                >  1:1232540/1‑71 (MQ=255)
                     aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                               >  1:3810863/1‑71 (MQ=255)
                     aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                               <  1:5348829/71‑1 (MQ=255)
                      aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                               >  1:1309038/1‑70 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgag                                                              <  1:1353721/54‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                            <  1:1602053/71‑1 (MQ=255)
                         caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgtt                                                         <  1:3004757/57‑1 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                    <  1:467898/45‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:1130947/46‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:3460134/57‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                    <  1:537169/43‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                        <  1:3609686/71‑1 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                                 >  1:3974433/1‑61 (MQ=255)
                              tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTAc                                       >  1:3787688/1‑70 (MQ=255)
                              tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:2924430/64‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                  >  1:474625/1‑41 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:3759093/52‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                     >  1:4083656/1‑53 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                            <  1:5174205/62‑1 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:3193288/1‑70 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:4746230/1‑70 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:93606/1‑70 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:2810953/1‑70 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                   >  1:5118424/1‑53 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 <  1:1769865/71‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:2608746/69‑1 (MQ=255)
                                    agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                <  1:4870941/71‑1 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                 >  1:2654201/1‑37 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                              >  1:1236762/1‑71 (MQ=255)
                                       aCCGCAATATAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             <  1:1567197/71‑1 (MQ=255)
                                       aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                             <  1:4418511/71‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                            <  1:5111981/71‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                            <  1:2141562/71‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                            <  1:2998278/71‑1 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                           <  1:188881/71‑1 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             >  1:4493052/1‑52 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                               <  1:4122532/49‑1 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                            <  1:327811/68‑1 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:561468/1‑70 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                   <  1:3209537/43‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:2880396/1‑68 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:2733729/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                      <  1:4337663/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       >  1:3141976/1‑70 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:5014434/36‑1 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:2613663/67‑1 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                    >  1:1469674/1‑70 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             >  1:4693697/1‑44 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:4342801/1‑56 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGCAGTCTCAGGAAAACca                  <  1:3496692/71‑1 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      >  1:3464898/1‑50 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                >  1:2808703/1‑56 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  >  1:909573/1‑70 (MQ=255)
                                                    gCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac                 >  1:1767617/1‑70 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                               <  1:4405767/39‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg               <  1:5288295/71‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACTTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  >  1:3742445/1‑67 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             <  1:5368097/40‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                             <  1:3651363/40‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTT‑ATTACGCTGGa                                 <  1:2292535/51‑1 (MQ=255)
                                                      tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                    <  1:2504529/65‑1 (MQ=255)
                                                       gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:911605/61‑1 (MQ=255)
                                                       gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa             >  1:1472053/1‑71 (MQ=255)
                                                       gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGTAGTCTCAGGAAAACCACAg               <  1:4823639/69‑1 (MQ=255)
                                                       gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  <  1:1329786/66‑1 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            >  1:3618187/1‑71 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         >  1:182804/1‑58 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa             <  1:5068661/70‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            <  1:5349622/71‑1 (MQ=255)
                                                           gCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt           >  1:181703/1‑69 (MQ=255)
                                                           gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa         <  1:5288259/71‑1 (MQ=255)
                                                            cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg        <  1:3981616/71‑1 (MQ=255)
                                                             tCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                <  1:1881430/46‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                            <  1:1618245/50‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt           <  1:1148492/67‑1 (MQ=255)
                                                               aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                              <  1:2049622/46‑1 (MQ=255)
                                                                   |                                                                     
CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  W3110S.gb/2809514‑2809650

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