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
A12 F133 I1 R1 102 83.9 4092546 96.1% 3932936 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,580,094 C→T D233N (GAT→AAT)  ydeM ← putative YdeN‑specific sulfatase‑maturating enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,580,0940CT98.8% 281.2 / ‑4.3 81D233N (GAT→AAT) ydeMputative YdeN‑specific sulfatase‑maturating enzyme
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (35/45);  total (36/45)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

CCTTGCAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGACATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACTATGACC  >  NC_000913/1579998‑1580193
                                                                                                |                                                                                                   
ccTTGCAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGtt                                                                                                  >  1:1104785/1‑100 (MQ=255)
ccTTGCAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGtt                                                                                                  >  2:1675232/1‑100 (MQ=255)
 cTTGCAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTAACGGATGAAAATTTCACCCACATTGttt                                                                                                 >  1:662965/1‑100 (MQ=255)
  ttGCAGGCCTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAACCTGACGGATGAAAATTTCACCCACATTGtttt                                                                                                >  2:1310843/1‑100 (MQ=255)
  ttGCAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGtttt                                                                                                <  2:185891/100‑1 (MQ=255)
   tGCAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGttttt                                                                                               <  1:1990113/100‑1 (MQ=255)
     cAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTaa                                                                                             <  1:1926167/100‑1 (MQ=255)
      aGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAAc                                                                                            <  2:856337/100‑1 (MQ=255)
      aGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAAc                                                                                            <  2:408654/100‑1 (MQ=255)
          cTCCTGGAAAATACAACTTGTATGCCCATTCCCCAAAAAACGTCTGACAAAGCTTTCAAACTGTCGGATGAAAATTTCACCCACATTGTTTTTAACCCAt                                                                                        <  1:127544/100‑1 (MQ=255)
            ccTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTg                                                                                      >  1:689842/1‑100 (MQ=255)
             cTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGc                                                                                     >  2:1607931/1‑100 (MQ=255)
              tGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCa                                                                                    >  1:1874485/1‑100 (MQ=255)
                  aaaTACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATaaa                                                                                <  2:1846293/100‑1 (MQ=255)
                      aCAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATg                                                                            <  2:1826251/100‑1 (MQ=255)
                      aCAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATg                                                                            >  2:555450/1‑100 (MQ=255)
                       cAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATg                                                                            >  1:1800225/1‑99 (MQ=255)
                        aaCTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGt                                                                          >  1:711574/1‑100 (MQ=255)
                        aaCTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGt                                                                          <  1:1822007/100‑1 (MQ=255)
                        aaCTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGt                                                                          <  2:836846/100‑1 (MQ=255)
                        aaCTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGt                                                                          <  1:586835/100‑1 (MQ=255)
                        aaCTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGt                                                                          <  1:124536/100‑1 (MQ=255)
                         aCTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGtt                                                                         >  1:607387/1‑100 (MQ=255)
                         aCTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGtt                                                                         >  2:142852/1‑100 (MQ=255)
                          cTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTg                                                                        <  2:1781504/100‑1 (MQ=255)
                          cTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTg                                                                        <  1:80595/100‑1 (MQ=255)
                           tGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGa                                                                       >  1:1662326/1‑100 (MQ=255)
                            ggTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGAc                                                                      >  1:266358/1‑100 (MQ=255)
                            ggTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGAc                                                                      <  2:1233953/100‑1 (MQ=255)
                             gTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACa                                                                     <  1:1583195/100‑1 (MQ=255)
                              tATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACAt                                                                    <  1:99860/100‑1 (MQ=255)
                              tATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACAt                                                                    <  1:1452470/100‑1 (MQ=255)
                               aTGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACAtg                                                                   <  2:1099351/100‑2 (MQ=255)
                               aTGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACAtg                                                                   >  2:1869272/1‑99 (MQ=255)
                                tGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACAtga                                                                  <  1:301241/100‑3 (MQ=255)
                                  cccATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAAc                                                                >  1:574608/1‑100 (MQ=255)
                                  cccATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAAc                                                                <  1:1188084/100‑1 (MQ=255)
                                  cccATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAAc                                                                >  1:94605/1‑100 (MQ=255)
                                    cATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACtt                                                              <  1:802391/100‑1 (MQ=255)
                                     aTTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTg                                                             <  1:142853/100‑1 (MQ=255)
                                      ttCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGc                                                            <  1:946684/100‑1 (MQ=255)
                                        ccccAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCa                                                          <  2:1662313/100‑1 (MQ=255)
                                         cccAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCAt                                                         >  1:1753485/1‑100 (MQ=255)
                                         cccAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCAt                                                         >  1:844149/1‑100 (MQ=255)
                                           cAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTGTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATaa                                                       >  2:1432552/1‑100 (MQ=255)
                                             aaaaaCGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGc                                                     <  1:691071/100‑1 (MQ=255)
                                             aaaaaCGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGACATAAACTTGCCATAAGc                                                     >  1:1222518/1‑100 (MQ=255)
                                                 aCGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTg                                                 >  2:1296022/1‑100 (MQ=255)
                                                   ggCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTggg                                               <  2:1782576/100‑1 (MQ=255)
                                                    gCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGa                                              <  2:844146/100‑1 (MQ=255)
                                                    gCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGa                                              <  2:432905/100‑1 (MQ=255)
                                                     cTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAg                                             <  1:1607943/100‑1 (MQ=255)
                                                        aCAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGca                                          >  1:597405/1‑100 (MQ=255)
                                                         cAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGcac                                         <  2:224571/100‑1 (MQ=255)
                                                         cAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGcac                                         <  1:1296029/100‑1 (MQ=255)
                                                         cAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATTG‑TTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGcaca                                        <  1:1310851/100‑1 (MQ=255)
                                                           aaGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAg                                       <  2:94604/100‑1 (MQ=255)
                                                           aaGCTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAg                                       >  1:1211781/1‑100 (MQ=255)
                                                              cTTTCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGaaa                                    >  1:1256779/1‑100 (MQ=255)
                                                               tttCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGaaaa                                   >  1:406165/1‑100 (MQ=255)
                                                                ttCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGaaaaa                                  <  2:597403/100‑1 (MQ=255)
                                                                ttCAAACTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGaaaaa                                  >  2:135578/1‑100 (MQ=255)
                                                                     aCTGACGGATGAAAATTTCACCCACATTGTTTTTAATCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAAt                             <  1:1432561/100‑1 (MQ=255)
                                                                     aCTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAAt                             <  1:1675245/100‑1 (MQ=255)
                                                                     aCTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAAt                             <  1:1869289/100‑1 (MQ=255)
                                                                     aCTGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAAt                             <  1:111884/100‑1 (MQ=255)
                                                                      ctaaCGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAAt                             <  2:1800209/96‑1 (MQ=255)
                                                                       tGACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa                           >  1:510455/1‑100 (MQ=255)
                                                                        gACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa                           <  1:132761/99‑1 (MQ=255)
                                                                        gACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGAt                          >  1:805254/1‑100 (MQ=255)
                                                                        gACGGATGAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGAt                          >  1:511771/1‑100 (MQ=255)
                                                                               gAAAATTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGaa                    >  1:440158/1‑99 (MQ=255)
                                                                                 aaaTTTCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAAtgt                 <  2:1104780/100‑1 (MQ=255)
                                                                                    tttCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGtt              <  2:406164/100‑1 (MQ=255)
                                                                                     ttCACCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTtc             >  1:80079/1‑100 (MQ=255)
                                                                                      tCACCCACATTGTTTTTAACCCATTGCATAAAAAGGGTTAACATGAACGTGCAATAAGACGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTtct            <  2:440157/100‑1 (MQ=255)
                                                                                        aCCCACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCa          >  1:537280/1‑100 (MQ=255)
                                                                                         cccACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCAc         >  1:393406/1‑100 (MQ=255)
                                                                                         cccACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCAc         >  1:1100438/1‑100 (MQ=255)
                                                                                          ccACATTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACt        >  1:277806/1‑100 (MQ=255)
                                                                                            acaTTGTTTTTAACCCATTGCATAAAAATGGTTGACATGAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACTAt      <  2:1874468/100‑1 (MQ=255)
                                                                                                cGTTTTTAACCCATTGCATAAAAATGGTTGACATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACTATGAcc  <  2:1222512/100‑1 (MQ=255)
                                                                                                |                                                                                                   
CCTTGCAGGACTCCTGGAAAATACAACTGGTATGCCCATTCCCCAAAAAACGGCTGACAAAGCTTTCAAACTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGACATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACTATGACC  >  NC_000913/1579998‑1580193

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A