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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 53.6% 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.gb2,809,5810GA53.6% 14.0 / 165.5 112G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (23/29);  new base A (33/27);  total (56/56)
Fisher's exact test for biased strand distribution p-value = 3.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

Only 100 of 116 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809513‑2809651
                                                                    |                                                                      
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                       <  1:5061340/70‑1 (MQ=255)
 cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                     <  1:672796/71‑1 (MQ=255)
 cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                      >  1:1027788/1‑70 (MQ=255)
     tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:2463563/1‑70 (MQ=255)
      cTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  >  1:2100794/1‑69 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgag                                                               <  1:4601147/69‑1 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:4445723/68‑1 (MQ=255)
            atgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgtt                                                          <  1:697765/71‑1 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        >  1:1172825/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       >  1:878085/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:2995038/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:2873791/71‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:666736/71‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      <  1:3342328/71‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGTAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:130007/59‑1 (MQ=255)
                  atgcaAAGCAAGATGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:4414454/1‑71 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTTAAGGCTCAGGGAATTAACga                                                                <  1:4948755/58‑1 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:2604523/53‑1 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   >  1:3564173/1‑70 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                 >  1:2394093/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   >  1:2917712/1‑69 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:4471591/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:4866297/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:2632434/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:13921/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:4675994/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:4836808/1‑71 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:2279470/1‑67 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:2449609/64‑1 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGt                                               <  1:1235896/71‑1 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    <  1:860479/66‑1 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                   >  1:4357604/1‑50 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:4328979/48‑1 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:2605038/48‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                  >  1:470354/1‑66 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                   >  1:5103371/1‑47 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:4503515/71‑1 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:3558901/71‑1 (MQ=255)
                            agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAtt                                          <  1:831005/71‑1 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:2480898/58‑1 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:204150/66‑1 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:1895111/71‑1 (MQ=255)
                              ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgag                                                               <  1:725883/48‑1 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                       >  1:4566920/1‑71 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                       >  1:1992960/1‑71 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     >  1:2235424/1‑53 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:5146035/50‑1 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                 >  1:661789/1‑71 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            >  1:5078965/1‑43 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:2677486/1‑67 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                               >  1:5144997/1‑71 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              >  1:2694208/1‑70 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                   <  1:1145400/64‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                   <  1:1721032/64‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:4898771/1‑63 (MQ=255)
                                           gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:2403032/1‑71 (MQ=255)
                                           gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:4499095/1‑71 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:382249/42‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:324521/54‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:2610905/1‑44 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:3671120/1‑59 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:2490410/1‑59 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                         >  1:4579036/1‑70 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                       <  1:63651/71‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                       <  1:301269/71‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      <  1:1718336/40‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      <  1:3719493/40‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                 >  1:2684511/1‑61 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                 >  1:4651474/1‑61 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                         <  1:1868450/69‑1 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:2237595/57‑1 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:4132305/57‑1 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:3546084/1‑40 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:1370848/1‑40 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:603437/1‑40 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:2806609/1‑40 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:2745307/1‑71 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     >  1:4991205/1‑39 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     >  1:4895245/1‑71 (MQ=255)
                                                   aTGCTGAAGGCTCAGTGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:2977991/1‑68 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:3245554/1‑68 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:3740691/71‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:2893421/71‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:3447212/71‑1 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                            <  1:276880/58‑1 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:1885782/70‑1 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                >  1:2025607/1‑68 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             >  1:3042496/1‑71 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          >  1:3599617/1‑58 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa              <  1:5087749/70‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             >  1:380083/1‑71 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:948337/71‑1 (MQ=255)
                                                           ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTc           <  1:3549331/71‑1 (MQ=255)
                                                            gCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa          <  1:4649322/71‑1 (MQ=255)
                                                            gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa          <  1:4558700/71‑1 (MQ=255)
                                                            gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa          <  1:843004/71‑1 (MQ=255)
                                                                    gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:3194617/1‑51 (MQ=255)
                                                                    gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:2733481/1‑51 (MQ=255)
                                                                    gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAGCCACAGTATTCAGCCTTCt   >  1:3657431/1‑70 (MQ=255)
                                                                    gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTg  <  1:4357376/71‑1 (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