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 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 54.8% 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.gb2,809,5810GA54.8% 44.9 / 204.3 148G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (37/29);  new base A (48/33);  total (85/63)
Fisher's exact test for biased strand distribution p-value = 7.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 154 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809513‑2809651
                                                                    |                                                                      
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                      >  1:207305/1‑71 (MQ=255)
  tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                     >  1:2994220/1‑70 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                    <  1:3387143/69‑1 (MQ=255)
        ttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                              >  1:1996973/1‑71 (MQ=255)
        ttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                              >  1:1340675/1‑71 (MQ=255)
        ttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                              >  1:11303/1‑71 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                   >  1:3718539/1‑65 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                               >  1:1645476/1‑69 (MQ=255)
          gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            >  1:3904914/1‑71 (MQ=255)
           catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            <  1:3728790/70‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:2070471/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:293977/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       >  1:968691/1‑71 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       >  1:2167363/1‑70 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                        >  1:41244/1‑67 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:3820957/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:602311/1‑71 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                    >  1:1377570/1‑54 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                 >  1:131486/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:1290766/1‑71 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   <  1:3292995/52‑1 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3040503/71‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                                   >  1:4362698/1‑65 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATTGCGTTg                                             <  1:8569/71‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              >  1:958166/1‑70 (MQ=255)
                          caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:312506/69‑1 (MQ=255)
                          caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            <  1:3965034/71‑1 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                >  1:4313873/1‑50 (MQ=255)
                            agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGTATTAACGAGACGTTGTTTa                                                     <  1:1062624/60‑1 (MQ=255)
                            agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     <  1:3431347/60‑1 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                  >  1:1969094/1‑62 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 <  1:1673215/63‑1 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                        >  1:2629715/1‑70 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:3604663/54‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAC‑‑‑ACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:81664/69‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:2615891/42‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:674911/1‑64 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                       <  1:4336432/69‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                      <  1:3620155/70‑1 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                              >  1:2561738/1‑44 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                             >  1:250092/1‑61 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:1241879/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                         >  1:925065/1‑48 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:172450/1‑59 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                        >  1:191034/1‑63 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                        >  1:1537371/1‑63 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  <  1:1112098/36‑1 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                               >  1:3886197/1‑71 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                        >  1:1032828/1‑62 (MQ=255)
                                        aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:2286104/71‑1 (MQ=255)
                                        aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:3683907/71‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:2820560/1‑59 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                             <  1:2366/71‑1 (MQ=255)
                                           gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:1666138/1‑71 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:1451355/1‑70 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                         >  1:3124014/1‑70 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            >  1:501633/1‑35 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAtt                                          >  1:3412498/1‑53 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          >  1:3988962/1‑69 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:629338/71‑1 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:4144135/71‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                           <  1:2429185/35‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     >  1:3675146/1‑41 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:1035064/70‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        >  1:4560892/1‑70 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                                <  1:895480/46‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        >  1:3697092/1‑70 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              >  1:907228/1‑46 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     >  1:3410511/1‑71 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:35289/1‑69 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     >  1:1637081/1‑70 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                               >  1:4299874/1‑43 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:2917173/1‑49 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:722876/1‑71 (MQ=255)
                                                    tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:3465524/1‑70 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca                 <  1:2819398/70‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGAATCAACGAGACGTTGTTTATg                                                   >  1:2185624/1‑36 (MQ=37)
                                                       tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:3338664/62‑1 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                      <  1:1993442/48‑1 (MQ=255)
                                                        gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:1290426/61‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             >  1:3528654/1‑71 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:2555140/71‑1 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             <  1:1047922/70‑1 (MQ=255)
                                                          aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:1212534/71‑1 (MQ=255)
                                                           ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            >  1:1440266/1‑70 (MQ=255)
                                                           ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:15160/1‑46 (MQ=255)
                                                           ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                       >  1:2095324/1‑59 (MQ=255)
                                                             cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg         <  1:2321394/71‑1 (MQ=255)
                                                              tCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:3236854/1‑52 (MQ=255)
                                                              tCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa          <  1:1295681/69‑1 (MQ=255)
                                                              tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  <  1:3048238/45‑1 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                               <  1:1574844/46‑1 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                                >  1:3254658/1‑45 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCt      >  1:1382242/1‑71 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCt      >  1:1578109/1‑71 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCt      <  1:408098/71‑1 (MQ=255)
                                                                 gggaATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCtt     <  1:4578136/71‑1 (MQ=255)
                                                                  gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:3489073/45‑1 (MQ=255)
                                                                  gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                            >  1:2309225/1‑47 (MQ=255)
                                                                   ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCt   <  1:3495118/71‑1 (MQ=255)
                                                                    |                                                                      
ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809513‑2809651

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