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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,838,137 G→A *395* (TAG→TAA)  setC → putative arabinose efflux transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,838,1370GA100.0% 195.6 / NA 61*395* (TAG→TAA) setCputative arabinose efflux transporter
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/33);  total (28/33)

CGCGTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAGCTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAGGGGATGC  >  NC_000913/3838003‑3838272
                                                                                                                                      |                                                                                                                                       
cgcgTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                     <  1:184367/139‑1 (MQ=255)
 gcgTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCAc                                                                                                                                    <  1:839343/139‑1 (MQ=255)
           gATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGc                                                                                                                          >  2:697497/1‑139 (MQ=255)
                 cGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                     >  2:824130/1‑122 (MQ=255)
                 cGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                     <  1:824130/122‑1 (MQ=255)
                                 ggAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCa                                                                                                    >  2:1222038/1‑139 (MQ=255)
                                        tGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACagag                                                                                             <  2:349997/139‑1 (MQ=255)
                                            tGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                     >  1:1190886/1‑95 (MQ=255)
                                            tGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                     <  2:1190886/95‑1 (MQ=255)
                                                aTCTGGATCTACCATGCGTTGTTCTGGCAGGCGAGAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGGTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAATAGAGCCAGCCTc                                                                                     <  1:9599/139‑1 (MQ=255)
                                                  cTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGc                                                                                   >  1:743644/1‑139 (MQ=255)
                                                     gAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAt                                                                                >  1:1265575/1‑139 (MQ=255)
                                                         tACCGTGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAttttt                                                                            <  1:94156/139‑1 (MQ=255)
                                                         tACCATGCGTTGTTCTGGCTGGGGATAGGGATGTTTGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAAGAGAGCCATCCTCGCCAttttt                                                                            <  1:1281378/139‑1 (MQ=255)
                                                           ccATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgcg                                                                                                      <  1:248808/111‑1 (MQ=255)
                                                           ccATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgcg                                                                                                      >  2:248808/1‑111 (MQ=255)
                                                             aTGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGc                                                                                   <  2:345534/128‑1 (MQ=255)
                                                             aTGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGc                                                                                   >  1:345534/1‑128 (MQ=255)
                                                             aTGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTa                                                                        >  1:1181584/1‑139 (MQ=255)
                                                              tGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTAt                                                                       <  1:1222038/139‑1 (MQ=255)
                                                                cGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgcg                                                                                                      >  2:579336/1‑106 (MQ=255)
                                                                cGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgcg                                                                                                      <  1:579336/106‑1 (MQ=255)
                                                                  ttgttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                                   <  1:316833/139‑1 (MQ=255)
                                                                  ttgttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                                   <  1:697497/139‑1 (MQ=255)
                                                                   tgttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGc                                                                  >  1:1098113/1‑139 (MQ=255)
                                                                     ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgc                                                                                                       <  2:311874/100‑1 (MQ=255)
                                                                     ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgc                                                                                                       >  1:311874/1‑100 (MQ=255)
                                                                     ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGc                                                                  <  1:386395/137‑1 (MQ=255)
                                                                     ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGc                                                                  >  2:386395/1‑137 (MQ=255)
                                                                      tCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGt                                                                                                                                >  2:1266243/1‑74 (MQ=255)
                                                                      tCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGt                                                                                                                                <  1:1266243/74‑1 (MQ=255)
                                                                       ctggctggCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCt                                                                <  2:1172563/137‑1 (MQ=255)
                                                                       ctggctggCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCt                                                                >  1:1172563/1‑137 (MQ=255)
                                                                              gcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGATAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGcatacata                                                       <  1:374906/139‑1 (MQ=255)
                                                                              gcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGcatacata                                                       <  1:1230067/139‑1 (MQ=255)
                                                                               cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                     <  1:788116/60‑1 (MQ=255)
                                                                               cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                     >  2:788116/1‑60 (MQ=255)
                                                                                        tGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCt                                                                <  2:984913/120‑1 (MQ=255)
                                                                                        tGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCt                                                                >  1:984913/1‑120 (MQ=255)
                                                                                             ggTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTa                                        >  1:289952/1‑139 (MQ=255)
                                                                                                aTTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGc                                     <  2:1265575/139‑1 (MQ=255)
                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGc                                                                                                            >  2:1225416/1‑49 (MQ=255)
                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGc                                                                                                            <  1:1225416/49‑1 (MQ=255)
                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGc                                                                          >  2:773435/1‑83 (MQ=255)
                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGc                                                                          <  1:773435/83‑1 (MQ=255)
                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCAGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                                >  1:747020/1‑109 (MQ=255)
                                                                                                                   tgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCAGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                                <  2:747020/109‑1 (MQ=255)
                                                                                                                     tttATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTccac                <  1:75010/139‑1 (MQ=255)
                                                                                                                       tattaAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCa                                    <  1:928711/117‑1 (MQ=255)
                                                                                                                       tatgaAAGATATTTAACTCAGCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCa                                    >  2:928711/1‑117 (MQ=255)
                                                                                                                        attaAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTg                                                                           <  1:1251186/77‑1 (MQ=255)
                                                                                                                        attaAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTg                                                                           >  2:1251186/1‑77 (MQ=255)
                                                                                                                               atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGc                                     >  1:1266926/1‑108 (MQ=255)
                                                                                                                               atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGc                                     <  2:1266926/108‑1 (MQ=255)
                                                                                                                               atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgggg      >  1:506186/1‑139 (MQ=255)
                                                                                                                               atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgggg      >  2:745269/1‑139 (MQ=255)
                                                                                                                                 atTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCACCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTc                   <  2:51259/124‑1 (MQ=255)
                                                                                                                                 atTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCACCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTc                   >  1:51259/1‑124 (MQ=255)
                                                                                                                                   ttAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgg        >  2:1370571/1‑133 (MQ=255)
                                                                                                                                   ttAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAGGGGATGc  <  2:289952/139‑1 (MQ=255)
                                                                                                                                   ttAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCAGGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgg        <  1:1370571/133‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                       
CGCGTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAGCTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAGGGGATGC  >  NC_000913/3838003‑3838272

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A