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 F56 I1 R1 165 53.8 2611523 96.4% 2517508 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,673,475 A→G G9G (GGT→GGC)  mdtJ ← multidrug efflux system transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,673,4750AG97.4% 257.3 / ‑2.0 76G9G (GGT→GGC) mdtJmultidrug efflux system transporter
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (38/36);  total (39/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.31e-01

AAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAG  >  NC_000913/1673378‑1673571
                                                                                                 |                                                                                                
aaaTCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGcc                                                                                                <  2:121839/100‑1 (MQ=255)
 aaTCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCt                                                                                               <  2:1295418/100‑1 (MQ=255)
  atcatcACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCta                                                                                              >  1:473527/1‑100 (MQ=255)
  atcatcACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCta                                                                                              >  1:36367/1‑100 (MQ=255)
     atcaCCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCtaata                                                                                           <  1:951384/100‑1 (MQ=255)
     atcaCCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCtaata                                                                                           <  1:193016/100‑1 (MQ=255)
       caCCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATaaa                                                                                         >  1:1061998/1‑100 (MQ=255)
         ccAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAAt                                                                                       >  1:217074/1‑100 (MQ=255)
         ccAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAAt                                                                                       <  2:1190433/100‑1 (MQ=255)
          cAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATc                                                                                      >  1:220452/1‑100 (MQ=255)
           aGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATcc                                                                                     <  2:803817/100‑1 (MQ=255)
              aTTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCaat                                                                                  >  2:732483/1‑100 (MQ=255)
               ttAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCaat                                                                                  <  1:570458/99‑1 (MQ=255)
                 aaaaTAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCaataaa                                                                               >  2:663542/1‑100 (MQ=255)
                     tAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAAtata                                                                           <  2:1124267/100‑1 (MQ=255)
                       atgccgccATTCCCCTCACTGACGCTCGCCCAGTTCATGGACAGCGCACCGGTAATTTCTTTAGCAATAGTCAGGCCTAATAAAATCCAATAAAtata                                                                           >  2:711653/3‑98 (MQ=255)
                       aaGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACa                                                                         >  1:992586/1‑100 (MQ=255)
                          ccgccATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTg                                                                      >  1:903055/1‑100 (MQ=255)
                          ccgccATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTg                                                                      <  1:996594/100‑1 (MQ=255)
                           cgccATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGt                                                                     >  2:229793/1‑100 (MQ=255)
                           cgccATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGt                                                                     <  1:351073/100‑1 (MQ=255)
                              cttttCCCTCACTAACGCTCGCCCATTTCATTGACAGCGTACTGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCt                                                                  >  1:883605/3‑100 (MQ=255)
                              cATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCt                                                                  <  1:1099425/100‑1 (MQ=255)
                              cATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCt                                                                  <  1:537380/100‑1 (MQ=255)
                                  tCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTtctc                                                              >  2:1173586/1‑100 (MQ=255)
                                   cccTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTcc                                                             >  2:461424/1‑100 (MQ=255)
                                    ccTCGCTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAACATCCAATAAATATACATTGTCCTTCTCCt                                                            <  1:584157/100‑1 (MQ=255)
                                     cTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTg                                                           >  1:190149/1‑100 (MQ=255)
                                       cACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCa                                                         <  2:1011556/100‑1 (MQ=255)
                                         cTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAag                                                       >  2:270590/1‑100 (MQ=255)
                                         cTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAag                                                       >  1:521392/1‑100 (MQ=255)
                                           gACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAagag                                                     <  2:1061988/100‑1 (MQ=255)
                                           gACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAagag                                                     >  1:1157916/1‑100 (MQ=255)
                                           gACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAagag                                                     <  2:932331/100‑1 (MQ=255)
                                             cGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGaa                                                   <  1:324416/100‑1 (MQ=255)
                                                  gCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAattatt                                              >  1:338353/1‑100 (MQ=255)
                                                     cATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTAtttt                                            <  2:762198/99‑1 (MQ=255)
                                                     cATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTa                                           >  2:119/1‑100 (MQ=255)
                                                      aTTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTaa                                          >  1:843832/1‑100 (MQ=255)
                                                      aTTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTaa                                          <  2:220450/100‑1 (MQ=255)
                                                       tttCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAAt                                         <  2:1084349/100‑1 (MQ=255)
                                                       tttCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAAt                                         >  1:654771/1‑100 (MQ=255)
                                                       tttCATTGACAGCGTACCGGTAATTTATGTAGCACTAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGTATTCTTTTAAt                                         <  2:686410/100‑1 (MQ=255)
                                                        ttCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCATGCAAGAGAATTATTTTAAtt                                        >  2:278812/1‑100 (MQ=255)
                                                         tCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAAttt                                       >  2:153503/1‑100 (MQ=255)
                                                            ttGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCg                                    <  1:1007658/100‑1 (MQ=255)
                                                            ttGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCg                                    <  1:1015571/100‑1 (MQ=255)
                                                            ttGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCg                                    <  2:36366/100‑1 (MQ=255)
                                                            ttGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCg                                    <  2:176607/100‑1 (MQ=255)
                                                            ttGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCg                                    >  1:202554/1‑100 (MQ=255)
                                                             tGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAACATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTAGc                                   >  1:251279/1‑100 (MQ=255)
                                                              gccAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCt                                  <  1:1252388/98‑1 (MQ=255)
                                                              gACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCt                                  >  2:19766/1‑100 (MQ=255)
                                                              gACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCt                                  >  1:1200481/1‑100 (MQ=255)
                                                                cAGCGTACCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTa                                <  2:522532/100‑1 (MQ=255)
                                                                      aCCGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAg                          <  2:358667/100‑1 (MQ=255)
                                                                       ccGGTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGc                         >  2:1258952/1‑100 (MQ=255)
                                                                        cGGTAATTTCTGTAGCAATAGCCAGGCCTGATAAAATCTAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCg                        <  2:14170/100‑1 (MQ=255)
                                                                         ggTAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAAAGAATTATTTTAATTTTCGCTTAATTCAGCGa                       >  1:516880/1‑100 (MQ=255)
                                                                           tAATTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGaaa                     <  2:1157905/100‑1 (MQ=255)
                                                                            aaTTTCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAAc                    >  1:1049032/1‑100 (MQ=255)
                                                                            aaTTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAAc                    <  1:1067273/100‑1 (MQ=255)
                                                                              tttCTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCa                  <  1:19766/100‑1 (MQ=255)
                                                                               ccgatctgCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCaa                 <  2:143719/93‑1 (MQ=255)
                                                                                 cTGTAGCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCaaag               <  1:732488/100‑1 (MQ=255)
                                                                                      gCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCTCTTAATTCAGCGAAACCaaagtaaag          <  1:792096/100‑1 (MQ=255)
                                                                                      gCAATAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCaaagatcgg          >  1:143721/1‑95 (MQ=255)
                                                                                        aaTAGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTg        >  1:906039/1‑100 (MQ=255)
                                                                                           aGCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTc     >  1:948948/1‑100 (MQ=255)
                                                                                            gacAGGCCTAATACAATCCAATAAATATACAGTGTCCTTCTCGTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCa    >  1:880316/3‑100 (MQ=255)
                                                                                            gCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCACAGTAAAGTGGTCa    >  1:758402/1‑100 (MQ=255)
                                                                                            gCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCa    <  1:433272/100‑1 (MQ=255)
                                                                                            gCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCa    >  1:154601/1‑100 (MQ=255)
                                                                                            gCCAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCa    <  2:992577/100‑1 (MQ=255)
                                                                                              cAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAg  >  2:538953/1‑100 (MQ=255)
                                                                                              cAGGCCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAg  >  1:117586/1‑100 (MQ=255)
                                                                                                 |                                                                                                
AAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGCCAGACCTAATAAAATCCAATAAATATACATTGTCCTTCTCCTGCAAGAGAATTATTTTAATTTTCGCTTAATTCAGCGAAACCAAAGTAAAGTGGTCAAG  >  NC_000913/1673378‑1673571

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A